From s.newslists at gmail.com  Sun Dec  4 05:25:56 2011
From: s.newslists at gmail.com (Stefan)
Date: Sun, 4 Dec 2011 11:25:56 +0100
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <4E159971.9070509@ebi.ac.uk>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
Message-ID: <CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>

2011/7/7 Peter Rice <pmr at ebi.ac.uk>:
> Very close to release date next week, so hard to do anything immediately.

Hello to the list,

are there any news in plasmid documentation and in-silico cloning with
EMBOSS? In the last month I was asked 4 times if this is possible with
EMBOSS. People like it to work with EMBOSS and want to do that things
also with this suite.

I would be happy to hear any progress.

Thanks
Stefan

From pmr at ebi.ac.uk  Sun Dec  4 15:22:12 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Sun, 04 Dec 2011 20:22:12 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
Message-ID: <4EDBD674.9050409@ebi.ac.uk>

On 04/12/2011 10:25, Stefan wrote:
> 2011/7/7 Peter Rice<pmr at ebi.ac.uk>:
>> Very close to release date next week, so hard to do anything immediately.
>
> are there any news in plasmid documentation and in-silico cloning with
> EMBOSS? In the last month I was asked 4 times if this is possible with
> EMBOSS. People like it to work with EMBOSS and want to do that things
> also with this suite.

Can you give us some examples of what you would like to see? Examples 
always help us to design new applicatons.

We still only have cirdna, mainly because we are limited by the plplot 
graphics library (and would welcome suggestions of other graphics 
libraries we could try).

We have extended the capabilities by creating input files from some 
other applications.

regards,

Peter Rice
EMBOSS team

From pmr at ebi.ac.uk  Mon Dec  5 04:26:00 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 05 Dec 2011 09:26:00 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <4EDC8BDA.30006@fmi.ch>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
	<4EDBD674.9050409@ebi.ac.uk> <4EDC8BDA.30006@fmi.ch>
Message-ID: <4EDC8E28.7090702@ebi.ac.uk>

On 12/05/2011 09:16 AM, Hans-Rudolf Hotz wrote:
> Thanks to the Galaxy framework, our lab scientist are using more and
> more EMBOSS tools. Now, it would be very handy if there was an EMBOSS
> drawing tool (even a very simple one) which takes an embl or genbank
> file as input and creates something "colorful". By default each Key or
> Qualifier is given a specific color and shape (eg 'arrow'). And you can
> change them as options.

Interesting suggestion. Can you send an example of what you would like 
to see?

You can use your favourite drawing tool if you like, but it is OK if you 
draw it in crayon, scan it and send the image :-)

regards,

Peter Rice
EMBOSS team

From hrh at fmi.ch  Mon Dec  5 04:16:10 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Mon, 5 Dec 2011 10:16:10 +0100
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <4EDBD674.9050409@ebi.ac.uk>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
	<4EDBD674.9050409@ebi.ac.uk>
Message-ID: <4EDC8BDA.30006@fmi.ch>



On 12/04/2011 09:22 PM, Peter Rice wrote:
> On 04/12/2011 10:25, Stefan wrote:
>> 2011/7/7 Peter Rice<pmr at ebi.ac.uk>:
>>> Very close to release date next week, so hard to do anything
>>> immediately.
>>
>> are there any news in plasmid documentation and in-silico cloning with
>> EMBOSS? In the last month I was asked 4 times if this is possible with
>> EMBOSS. People like it to work with EMBOSS and want to do that things
>> also with this suite.
>
> Can you give us some examples of what you would like to see? Examples
> always help us to design new applicatons.
>

Hi Peter and Stefan

Please allow me to jump in and tell you about our situation:

Our wet lab scientist use depending (which lab/university they are 
coming from) a combination of old commercial products (which we can 
still use thank to the perpetual licenses) and free/open source products 
like 'Serial Cloner', 'Ape', 'Gentle', etc

I constantly 'preach' how vital it is to make sure you safe each 
sequence/plasmid/etc not only in the tool specific format, but also in a 
text format like embl or genbank, where all the annotation is stored in 
the Feature Table

Thanks to the Galaxy framework, our lab scientist are using more and 
more EMBOSS tools. Now, it would be very handy if there was an EMBOSS 
drawing tool (even a very simple one) which takes an embl or genbank 
file as input and creates something "colorful". By default each Key or 
Qualifier is given a specific color and shape (eg 'arrow'). And you can 
change them as options.

I hope this works as a use case?


Regards, Hans



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland

> We still only have cirdna, mainly because we are limited by the plplot
> graphics library (and would welcome suggestions of other graphics
> libraries we could try).
>
> We have extended the capabilities by creating input files from some
> other applications.
>
> regards,
>
> Peter Rice
> EMBOSS team
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

From p.j.a.cock at googlemail.com  Mon Dec  5 05:08:59 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Dec 2011 10:08:59 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <4EDC8E28.7090702@ebi.ac.uk>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
	<4EDBD674.9050409@ebi.ac.uk> <4EDC8BDA.30006@fmi.ch>
	<4EDC8E28.7090702@ebi.ac.uk>
Message-ID: <CAKVJ-_7YeStqhNQjkOp0NW=qfD97QdH_WAh59wLSQuty-vWLGg@mail.gmail.com>

On Mon, Dec 5, 2011 at 9:26 AM, Peter Rice <pmr at ebi.ac.uk> wrote:
> On 12/05/2011 09:16 AM, Hans-Rudolf Hotz wrote:
>>
>> Thanks to the Galaxy framework, our lab scientist are using more and
>> more EMBOSS tools. Now, it would be very handy if there was an EMBOSS
>> drawing tool (even a very simple one) which takes an embl or genbank
>> file as input and creates something "colorful". By default each Key or
>> Qualifier is given a specific color and shape (eg 'arrow'). And you can
>> change them as options.
>
> Interesting suggestion. Can you send an example of what you
> would like to see?
>
> You can use your favourite drawing tool if you like, but it is OK if
> you draw it in crayon, scan it and send the image :-)
>

I use Biopython's GenomeDiagram for this sort of thing, which
internally uses a Python library called ReportLab which can
produce PDF, SVG, PNG, etc. Sadly I doubt that would be
suitable for EMBOSS which would really want a C library.

GenomeDiagram has the notion of tracks - which can be
useful for separating different types of features which would
otherwise overlap (e.g. gene/mRNA/CDS) and other tricks.
It also has some defaults about which feature qualifiers
to use as the feature name (e.g. gene, locustag).

I have considered writing a Galaxy tool to take an EMBL or
GenBank file and produce a picture, but haven't got round
to it yet.

Anyway, there may be some useful ideas for layout here
if nothing else.

Peter

From pmr at ebi.ac.uk  Mon Dec  5 05:19:41 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 05 Dec 2011 10:19:41 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <CAKVJ-_7YeStqhNQjkOp0NW=qfD97QdH_WAh59wLSQuty-vWLGg@mail.gmail.com>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
	<4EDBD674.9050409@ebi.ac.uk> <4EDC8BDA.30006@fmi.ch>
	<4EDC8E28.7090702@ebi.ac.uk>
	<CAKVJ-_7YeStqhNQjkOp0NW=qfD97QdH_WAh59wLSQuty-vWLGg@mail.gmail.com>
Message-ID: <4EDC9ABD.2020605@ebi.ac.uk>

On 12/05/2011 10:08 AM, Peter Cock wrote:
> I use Biopython's GenomeDiagram for this sort of thing, which
> internally uses a Python library called ReportLab which can
> produce PDF, SVG, PNG, etc. Sadly I doubt that would be
> suitable for EMBOSS which would really want a C library.
>
> GenomeDiagram has the notion of tracks - which can be
> useful for separating different types of features which would
> otherwise overlap (e.g. gene/mRNA/CDS) and other tricks.
> It also has some defaults about which feature qualifiers
> to use as the feature name (e.g. gene, locustag).

The EMBOSS solution to tracks would probably use the Sequence Ontology 
to define the tracks, and use features below some specified tag (or set 
of tags) for each track.

We can apply the same tracks to showfeat (the text display of features)

Tracks also simplify the issues of colours for features.

lindna has code for rendering features withg scaling and avoiding 
overlaps which we could also, I hope, reuse.

Maybe not for the next release (release date 15th January, but code 
freeze before Christmas) but we can provide applications for testing by 
anyone interested after the release.

regards,

Peter Rice
EMBOSS Team


From david.bauer at bayer.com  Mon Dec  5 04:38:34 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Mon, 5 Dec 2011 10:38:34 +0100
Subject: [EMBOSS] Plasmid drawing
Message-ID: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>

Hi Peter,

I think Stefan means not only the drawing of plasmid maps but the creation 
of new constructs in the computer before doing it at the bench.
This is a field where there are currently only commercial packages 
available like VectorNTI and Clone Manager (
http://www.scied.com/pr_cmpro.htm) etc.
Clone manager is there since the times of MS-DOS but the prices have 
increased substantially. They used to advertise the software with the 
slogan: "It costs only as much as a cloning kit for the lab" - which was 
in the range of 300,-USD.

The most important functions, which I think should be implement first are 
the cloning operations.
So e.g. 
- take plasmid1, open the multi cloning site with BamHI and EcoRI
- take plasmid2, cut out a fragment with BglII and EcoRI
- ligate the fragment from plasmid2 into plasmid1
        (BamHI and BglII have compatible ends which can be ligated, so an 
algorithm is needed to check this)
- draw a map of the newly created plasmid3
This is a rather simple example.
There can be more complex procedures like Klenow fill in (blunt end 
ligation of incompatible restriction sites) or the use of more than 2 
fragments in one ligation.

I think most of the functions needed for this are already present in 
EMBOSS.
It shouldn't be so complicated to create an application which uses 
functions from restrict, cutseq, pasteseq to accomplish the above 
mentioned task.
Although it's probably not so trivial to make this happen before the 
release next week ;-)

Cheers,
David.




Peter Rice <pmr at ebi.ac.uk> 
Gesendet von: emboss-bounces at lists.open-bio.org
04/12/2011 21:22

An
Stefan <s.newslists at gmail.com>
Kopie
emboss at lists.open-bio.org
Thema
Re: [EMBOSS] Plasmid drawing






On 04/12/2011 10:25, Stefan wrote:
> 2011/7/7 Peter Rice<pmr at ebi.ac.uk>:
>> Very close to release date next week, so hard to do anything 
immediately.
>
> are there any news in plasmid documentation and in-silico cloning with
> EMBOSS? In the last month I was asked 4 times if this is possible with
> EMBOSS. People like it to work with EMBOSS and want to do that things
> also with this suite.

Can you give us some examples of what you would like to see? Examples 
always help us to design new applicatons.

We still only have cirdna, mainly because we are limited by the plplot 
graphics library (and would welcome suggestions of other graphics 
libraries we could try).

We have extended the capabilities by creating input files from some 
other applications.

regards,

Peter Rice
EMBOSS team
_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss


From s.newslists at gmail.com  Mon Dec  5 05:44:34 2011
From: s.newslists at gmail.com (Stefan)
Date: Mon, 5 Dec 2011 11:44:34 +0100
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>
References: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>
Message-ID: <CAECtV7M+PWO+_cgV8BH0cdYEu0Kx9yTzhg3NVbJT_d2KC9=_PA@mail.gmail.com>

> I think Stefan means not only the drawing of plasmid maps but the creation of new constructs in the computer before doing it at the bench.
What David wrote is exactly what I wanted to explain with "in-silico cloning".
With plasmid documentation I meant that it is possible to draw
aplasmid with features and restriction sites.
Thanks

From pmr at ebi.ac.uk  Mon Dec  5 08:23:23 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 05 Dec 2011 13:23:23 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <CB027D1E.5D88%hrh@fmi.ch>
References: <CB027D1E.5D88%hrh@fmi.ch>
Message-ID: <4EDCC5CB.2090402@ebi.ac.uk>

On 05/12/2011 12:52, Hotz, Hans-Rudolf wrote:

> "cirdna" and "lindna" are nice and do their job most of the time. In my
> view, the problem is the input file format. Maybe a converter from
> embl/genbank to *.crip or *.linp would be a good start? Or adding the those
> formats to the output options of seqret?

We do already support "draw" an a report output format.

If we add it as a feature output format you can use featcopy (or seqret 
-feat) to create a cirdna or lindna input file.

We can then work on the feature format to add extra information by 
feature type.

We could also add an application to merge a set of feature inputs so you 
could combine genbank/embl files with restriction map output, then use 
the results as input.

I will see what I can do for the next release.

Thanks for the very helpful suggestions

Peter Rice
EMBOSS Team

From marko at cryst.bioc.cam.ac.uk  Mon Dec  5 08:10:06 2011
From: marko at cryst.bioc.cam.ac.uk (Marko Hyvonen)
Date: Mon, 5 Dec 2011 13:10:06 +0000 (GMT)
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>
References: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>
Message-ID: <alpine.LNX.2.00.1112051300590.5959@mackerel.bioc.cam.ac.uk>



I would find this kind of in silico cloning great addition to EMBOSS.

As an example of (a free?) drawing program for plasmids, I use PlasMapper 
(http://wishart.biology.ualberta.ca/PlasMapper/ , source code is at least 
available on the site). Here is an example I made from their own selection 
of plasmids (hopefully valid link for a while still):
  http://wishart.biology.ualberta.ca/PlasMapper/jsp/displayPlasmidMap.jsp?fileName=plasMap26_1323082022185.png&fileFormat=png

I like the fact that it includes a number of predefined features in 
plasmids as built-ins, so that you only need to include the "unique" 
features in your own plasmids (and I am sure the set of built-ins could be 
expanded much further). Outputs svg too, which is brilliant for editing 
later on.

Marko


On Mon, 5 Dec 2011, david.bauer at bayer.com wrote:

> Hi Peter,
>
> I think Stefan means not only the drawing of plasmid maps but the creation
> of new constructs in the computer before doing it at the bench.
> This is a field where there are currently only commercial packages
> available like VectorNTI and Clone Manager (
> http://www.scied.com/pr_cmpro.htm) etc.
> Clone manager is there since the times of MS-DOS but the prices have
> increased substantially. They used to advertise the software with the
> slogan: "It costs only as much as a cloning kit for the lab" - which was
> in the range of 300,-USD.
>
> The most important functions, which I think should be implement first are
> the cloning operations.
> So e.g.
> - take plasmid1, open the multi cloning site with BamHI and EcoRI
> - take plasmid2, cut out a fragment with BglII and EcoRI
> - ligate the fragment from plasmid2 into plasmid1
>        (BamHI and BglII have compatible ends which can be ligated, so an
> algorithm is needed to check this)
> - draw a map of the newly created plasmid3
> This is a rather simple example.
> There can be more complex procedures like Klenow fill in (blunt end
> ligation of incompatible restriction sites) or the use of more than 2
> fragments in one ligation.
>
> I think most of the functions needed for this are already present in
> EMBOSS.
> It shouldn't be so complicated to create an application which uses
> functions from restrict, cutseq, pasteseq to accomplish the above
> mentioned task.
> Although it's probably not so trivial to make this happen before the
> release next week ;-)
>
> Cheers,
> David.
>
>
>
>
> Peter Rice <pmr at ebi.ac.uk>
> Gesendet von: emboss-bounces at lists.open-bio.org
> 04/12/2011 21:22
>
> An
> Stefan <s.newslists at gmail.com>
> Kopie
> emboss at lists.open-bio.org
> Thema
> Re: [EMBOSS] Plasmid drawing
>
>
>
>
>
>
> On 04/12/2011 10:25, Stefan wrote:
>> 2011/7/7 Peter Rice<pmr at ebi.ac.uk>:
>>> Very close to release date next week, so hard to do anything
> immediately.
>>
>> are there any news in plasmid documentation and in-silico cloning with
>> EMBOSS? In the last month I was asked 4 times if this is possible with
>> EMBOSS. People like it to work with EMBOSS and want to do that things
>> also with this suite.
>
> Can you give us some examples of what you would like to see? Examples
> always help us to design new applicatons.
>
> We still only have cirdna, mainly because we are limited by the plplot
> graphics library (and would welcome suggestions of other graphics
> libraries we could try).
>
> We have extended the capabilities by creating input files from some
> other applications.
>
> regards,
>
> Peter Rice
> EMBOSS team
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>


  _____________________________________

  Marko Hyvonen
  Department of Biochemistry, University of Cambridge
  marko at cryst.bioc.cam.ac.uk
  http://www-cryst.bioc.cam.ac.uk/groups/hyvonen
  tel:    +44-(0)1223-766 044
  mobile: +44-(0)7796-174 877
  fax:    +44-(0)1223-766 002
  --------------------------------------

From hmenager at pasteur.fr  Mon Dec  5 11:14:20 2011
From: hmenager at pasteur.fr (=?ISO-8859-1?Q?Herv=E9_M=E9nager?=)
Date: Mon, 05 Dec 2011 17:14:20 +0100
Subject: [EMBOSS] ORF selection with EMBOSS
Message-ID: <4EDCEDDC.3020200@pasteur.fr>

Hi,
I have been using transeq and checktrans to find ORFs in DNA sequences. 
I have an question regarding the selection of the ORFs in case 
checktrans finds multiple ones in the result of transeq: I would like to 
select the longest one automatically (assuming it is the correct one). 
Is there any existing tool in EMBOSS (or alternatively in any Bio* 
library) that does this job?
Cheers,
Herv?

From mathog at caltech.edu  Mon Dec  5 11:35:31 2011
From: mathog at caltech.edu (mathog)
Date: Mon, 05 Dec 2011 08:35:31 -0800
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
Message-ID: <a5f593a8b406dc04b53acc6ffc899ea7@saf.bio.caltech.edu>

On Sun, 4 Dec 2011 11:25:56 +0100, Stefan wrote:

> are there any news in plasmid documentation and in-silico cloning 
> with
> EMBOSS?

Pierre Lindenbaum wrote a nice little program called "cloneit" for 
figuring out cloning
strategies.  That is, specifically what series of reactions to use to 
insert a particular
piece of DNA into a vector.  Not sure if that is what you mean by 
"in-silico cloning" or not. There is
a separate cgi version for web use.  Here is the paper:

http://www.ncbi.nlm.nih.gov/pubmed/9682060?dopt=Abstract

The original distribution site is long since off line, but the code 
says that it may
be redistributed (and incorporated in noncommercial software, but see 
the exact wording
for details.)  Anyway, if anybody wants to have a look, I packed up our 
copies and put
them here:

http://saf.bio.caltech.edu/pub/software/molbio/cloneit.tar.gz
http://saf.bio.caltech.edu/pub/software/molbio/cloneitcgi.tar.gz

This is not a graphics program, it is a reaction planning program.

As for the graphical output of plasmid diagrams, historically none of 
the drawing programs
does exactly what the end users want.  (These get closer and closer, 
but never quite cover
all the bases).  For that reason it is really important that the 
graphics driver be able to
output to an object format that can then be imported into a drawing 
program and edited there.
Modifying an image never turns out as nicely.  When going to object 
formats it is key that
text remain text and not be converted into line segments or
paths. Users get really frustrated when they can't edit labels or 
change fonts or font sizes.
Locally we have a hacked up GCG driver that emits cgm format for the 
GCG drawing programs.
Nowadays going to SVG would make more sense.

While it is sometimes possible to read PDF back into a drawing program 
like inkscape, text imported
that way is very hit and miss, mostly miss.  Often it comes through 
with each
letter as a separate text object, which is no fun at all to work with.  
Other times it will come in with
each letter separately kerned, and when that kerning is removed, the 
text jumps all over the place in
unpredictable ways.  Why would you remove the kerning?  Because there 
is another bug/limitation
in inkscape where kerned text is automatically converted to images when 
exporting to emf or wmf format,
as when trying to move that image into a powerpoint document.  Moving 
rotated text between various
programs is the most unreliable operation, as far as I can tell.  For 
instance, I have never found
a way to get text which runs at an angle other than 0 degrees from 
inskcape into powerpoint with that
angle intact.  The text comes through, but the angle is lost.

Regards,


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

From Scott.Markel at accelrys.com  Mon Dec  5 20:14:19 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Mon, 5 Dec 2011 17:14:19 -0800
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>

We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.

Here are EMBOSS command lines for embossversion and acdtable.

> embossversion
Reports the current EMBOSS version number
6.4.0.2

> acdtable fuzzpro -help -verbose >& fuzzpro_6.4.0.html

And here are the three sets of tag mismatches in the HTML.  All involve an opening <th> and a closing </td>.

Lines 66-9:

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>"-sequence" associated seqall qualifiers </td> </tr>

Lines 183-6:

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>"-pattern" associated pattern qualifiers </td> </tr>

Lines 212-5:

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>"-outfile" associated report qualifiers </td> </tr>

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect? email:? smarkel at accelrys.com
Accelrys (Pipeline Pilot R&D)?????? mobile: +1 858 205 3653
10188 Telesis Court, Suite 100????? voice:? +1 858 799 5603
San Diego, CA 92121???????????????? fax:??? +1 858 799 5222
USA???????????????????????????????? web:??? http://www.accelrys.com

http://www.linkedin.com/in/smarkel
Secretary, Board of Directors:
??? International Society for Computational Biology
Chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics





From cjfields at illinois.edu  Mon Dec  5 21:03:35 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 6 Dec 2011 02:03:35 +0000
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>
Message-ID: <BD5A1F3D-0EE3-4B8E-9E54-947CCD8D2CCE@illinois.edu>

Scott, is this something that needs to be addressed on the bioperl end?

chris

On Dec 5, 2011, at 7:14 PM, Scott Markel wrote:

> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.
> 
> Here are EMBOSS command lines for embossversion and acdtable.
> 
>> embossversion
> Reports the current EMBOSS version number
> 6.4.0.2
> 
>> acdtable fuzzpro -help -verbose >& fuzzpro_6.4.0.html
> 
> And here are the three sets of tag mismatches in the HTML.  All involve an opening <th> and a closing </td>.
> 
> Lines 66-9:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-sequence" associated seqall qualifiers </td> </tr>
> 
> Lines 183-6:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-pattern" associated pattern qualifiers </td> </tr>
> 
> Lines 212-5:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-outfile" associated report qualifiers </td> </tr>
> 
> Scott
> 
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> San Diego, CA 92121                 fax:    +1 858 799 5222
> USA                                 web:    http://www.accelrys.com
> 
> http://www.linkedin.com/in/smarkel
> Secretary, Board of Directors:
>     International Society for Computational Biology
> Chair: ISCB Publications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
> 
> 
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From pandey.gaurav at gmail.com  Mon Dec  5 23:07:10 2011
From: pandey.gaurav at gmail.com (Gaurav Pandey)
Date: Mon, 5 Dec 2011 23:07:10 -0500
Subject: [EMBOSS] Research opportunities in systems biology at Mt. Sinai
	School of Medicine
Message-ID: <CAMqOHCw34+o7iWwW_RZ3HyhY013WP=iiSkvO9nqvyrQoqH4=rQ@mail.gmail.com>

Please forward this announcement to potential applicants if it is not
directly applicable to you. Apologies for cross-posting.



---------------------------



The Institute for Genomics and Multi-scale Biology (multiscale.mssm.edu) at
the Mount Sinai School of Medicine (www.mssm.edu) in New York City is
seeking applications from enthusiastic and capable researchers for
positions at Ph.D., postdoc and staff level. The Institute is the hub of
genomics research at Mount Sinai, collaborating with13 other
disease-oriented and core-technology-based institutes, and aims to
translate genomics-based science into actionable medical knowledge. The
Institute's faculty members have expertise in a wide range of areas such as
machine learning, biostatistics, genetics, genomics, sequencing technology,
data science, and high-performance computing (HPC).



We wish to recruit capable and motivated graduate students, post-doctoral
associates, and research staff members. Please look at the detailed
announcement at the end of this email providing information on specific
requirements for these positions. PhD and MD/PhD applicants should consult
the requirements of the Graduate School at Mount Sinai (
http://www.mssm.edu/education/graduate-school) for application and
potential admission. Others should send their requisite application
material (see below) to multiscale.biology at mssm.edu. For more information,
visit the Institute's website (multiscale.mssm.edu) and/or email
multiscale.biology at mssm.edu.



-------------------------------

The Multiscale Institute is actively recruiting graduate students,
post-doctoral scholars and technical staff interested in working on
challenging and important problems in computational systems biology,
especially with a focus on translating this work to the medical domain.

Prospective Students

If you are a prospective MD (
http://www.mssm.edu/education/medical-education/programs/md-program), Ph.D.
or MD/Ph.D. (http://www.mssm.edu/education/graduate-school) student, the
Multiscale Institute provides a cutting-edge research environment, strong
mentorship and comprehensive training in computational biology. Please
check out the various degree programs within the Mount Sinai School of
Medicine, and for Ph.D. students, the Genetics and Genomics Training Area
(http://www.mssm.edu/education/graduate-school/degrees-and-programs/phd-program/multidisciplinary-training-areas/genetics-and-genomic-sciences)<file://localhost/about/blank>in
particular, for more information. Alternatively, contact us directly
at
multiscale.biology at mssm.edu for information.

The Multiscale Institute faculty members have backgrounds in Computer
Science, Engineering, Statistics, Mathematics, Physics, Genetics, Molecular
Biology, and related disciplines, and are looking for students from all of
those fields. The essential requirement is an interest in and capability of
thinking about real-world problems in quantitative terms. Additional
desired (but not essential) characteristics will be (1) a background in
biology, acquired through courses and/or research work and/or (2)
experience with data-intensive real-world problems (from any domain) and/or
(3) experience with programming.

If you are not yet applying to graduate school, we recommend you to check
out SURP (
http://www.mssm.edu/education/graduate-school/degrees-and-programs/summer-undergraduate-research-program),
the Summer Undergraduate Research Program at Mount Sinai.

Prospective Post-doctoral Scholars

At the Multiscale Institute, you will have a chance to work with world
class scientists and engineers tackling important and highly visible
problems in computational biology, with an emphasis on translating such
work into the medical domain. Some example targets of the Institute are
identifying actionable biomarkers and therapeutics for complex human
diseases.

Candidates should have a recent PhD and/or MD degree in a science,
technology, engineering or medical field, and discipline and high
motivation to pursue independent research in computational biology.
Applicants are expected to have a solid background in programming and
computational techniques, with a working knowledge of molecular biology and
genetics being highly desirable. To apply, send a CV, a research statement
and contact information for three referees to the
multiscale.biology at mssm.edu. More information about postdoctoral training
at Mt. Sinai can be found at the Office of Postdoctoral Affairs (
http://www.mssm.edu/education/postdoctoral-training).

Technical Staff

We are looking for engineers and scientists to help Institute researchers
extract clinical insight from petabyte-scale data sets. The ideal candidate
will be comfortable in an academic environment, and will bring energy and
creativity to the Institute?s work. In particular, the applicant is
expected to have substantial experience working with big data and its
associated infrastructure, including data retrieval from a variety of
data-stores, statistics with R/C++/Java etc., and visualization for the web
and print. A biology background is desired, but not required; we are
primarily looking for people with strong data analysis and software
engineering skills. To apply, send your resume to
multiscale.biology at mssm.edu



-- 
Gaurav Pandey, Ph.D.
Assistant Professor
Department of Genetics and Genomic Sciences
Mount Sinai School of Medicine, New York City
http://www.mssm.edu/profiles/gaurav-pandey


From pmr at ebi.ac.uk  Tue Dec  6 03:52:33 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 06 Dec 2011 08:52:33 +0000
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <5ACBA19439E77B43A06F4CAB897EC97702FA783783@EXCH1-COLO.accelrys.net>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783783@EXCH1-COLO.accelrys.net>
Message-ID: <4EDDD7D1.4030001@ebi.ac.uk>

Dear Scott,

On 06/12/2011 00:35, Scott Markel wrote:
> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.

> And here are the three sets of tag mismatches in the HTML.  All involve an opening<th>  and a closing</td>.

Oops. Well spotted. Simple fix in ajax/acd/ajacd.c ... we have a new 
release due in January when our current funding ends, but will look to 
release a patch for you.

 From the version number, was this mEMBOSS you were using?

regards,

Peter Rice
EMBOSS Team

From jison at ebi.ac.uk  Tue Dec  6 06:00:15 2011
From: jison at ebi.ac.uk (Jon Ison)
Date: Tue, 6 Dec 2011 11:00:15 -0000 (UTC)
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <4EDCEDDC.3020200@pasteur.fr>
References: <4EDCEDDC.3020200@pasteur.fr>
Message-ID: <36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>

Hi Herv?

Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the longest
ORF then that should be an easy enough option to add.

Cheers

Jon


> Hi,
> I have been using transeq and checktrans to find ORFs in DNA sequences.
> I have an question regarding the selection of the ORFs in case
> checktrans finds multiple ones in the result of transeq: I would like to
> select the longest one automatically (assuming it is the correct one).
> Is there any existing tool in EMBOSS (or alternatively in any Bio*
> library) that does this job?
> Cheers,
> Herv?
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From hmenager at pasteur.fr  Tue Dec  6 06:07:11 2011
From: hmenager at pasteur.fr (=?ISO-8859-1?Q?Herv=E9_M=E9nager?=)
Date: Tue, 06 Dec 2011 12:07:11 +0100
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
Message-ID: <4EDDF75F.8020400@pasteur.fr>

Hi Jon,

That's exactly what would make me happy. Assuming it makes it easier for 
you if I formulate officially this request, where do I need to send the 
request?

Herv?

On 12/06/2011 12:00 PM, Jon Ison wrote:
> Hi Herv?
>
> Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the longest
> ORF then that should be an easy enough option to add.
>
> Cheers
>
> Jon
>
>
>> Hi,
>> I have been using transeq and checktrans to find ORFs in DNA sequences.
>> I have an question regarding the selection of the ORFs in case
>> checktrans finds multiple ones in the result of transeq: I would like to
>> select the longest one automatically (assuming it is the correct one).
>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>> library) that does this job?
>> Cheers,
>> Herv?
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>


From jison at ebi.ac.uk  Tue Dec  6 06:11:01 2011
From: jison at ebi.ac.uk (Jon Ison)
Date: Tue, 6 Dec 2011 11:11:01 -0000 (UTC)
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <4EDDF75F.8020400@pasteur.fr>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
	<4EDDF75F.8020400@pasteur.fr>
Message-ID: <48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>

A note of it is already on the SourceForge "Feature Requests" ...

J:)



> Hi Jon,
>
> That's exactly what would make me happy. Assuming it makes it easier for
> you if I formulate officially this request, where do I need to send the
> request?
>
> Herv?
>
> On 12/06/2011 12:00 PM, Jon Ison wrote:
>> Hi Herv?
>>
>> Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the
>> longest
>> ORF then that should be an easy enough option to add.
>>
>> Cheers
>>
>> Jon
>>
>>
>>> Hi,
>>> I have been using transeq and checktrans to find ORFs in DNA sequences.
>>> I have an question regarding the selection of the ORFs in case
>>> checktrans finds multiple ones in the result of transeq: I would like to
>>> select the longest one automatically (assuming it is the correct one).
>>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>>> library) that does this job?
>>> Cheers,
>>> Herv?
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>
>>
>



From andrespinzon at gmail.com  Tue Dec  6 07:53:36 2011
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Tue, 6 Dec 2011 07:53:36 -0500
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
	<4EDDF75F.8020400@pasteur.fr>
	<48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>
Message-ID: <CACmy5HD6hydbvfEtXo7Pxnp3-YsLDkqt5k1_hp1Q75PouhM3AQ@mail.gmail.com>

Herve,
Have you tried using "getorf" and then "sizeseq"?
I think it will work. Then you could get the first sequence from the output.

Best,

On Tue, Dec 6, 2011 at 6:11 AM, Jon Ison <jison at ebi.ac.uk> wrote:
> A note of it is already on the SourceForge "Feature Requests" ...
>
> J:)
>
>
>
>> Hi Jon,
>>
>> That's exactly what would make me happy. Assuming it makes it easier for
>> you if I formulate officially this request, where do I need to send the
>> request?
>>
>> Herv?
>>
>> On 12/06/2011 12:00 PM, Jon Ison wrote:
>>> Hi Herv?
>>>
>>> Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the
>>> longest
>>> ORF then that should be an easy enough option to add.
>>>
>>> Cheers
>>>
>>> Jon
>>>
>>>
>>>> Hi,
>>>> I have been using transeq and checktrans to find ORFs in DNA sequences.
>>>> I have an question regarding the selection of the ORFs in case
>>>> checktrans finds multiple ones in the result of transeq: I would like to
>>>> select the longest one automatically (assuming it is the correct one).
>>>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>>>> library) that does this job?
>>>> Cheers,
>>>> Herv?
>>>> _______________________________________________
>>>> EMBOSS mailing list
>>>> EMBOSS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>
>>>
>>>
>>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



-- 
Andr?s Pinz?n


From hmenager at pasteur.fr  Tue Dec  6 09:20:11 2011
From: hmenager at pasteur.fr (=?UTF-8?B?SGVydsOpIE3DqW5hZ2Vy?=)
Date: Tue, 06 Dec 2011 15:20:11 +0100
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <CACmy5HD6hydbvfEtXo7Pxnp3-YsLDkqt5k1_hp1Q75PouhM3AQ@mail.gmail.com>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
	<4EDDF75F.8020400@pasteur.fr>
	<48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>
	<CACmy5HD6hydbvfEtXo7Pxnp3-YsLDkqt5k1_hp1Q75PouhM3AQ@mail.gmail.com>
Message-ID: <4EDE249B.7080207@pasteur.fr>

Hi Andres,
 From my point of view, it would do the job if I didn't have a _list_ of 
genes as an input: I hence need to input a list of genes and get as an 
output a list of the longest ORF computed for each gene. If I do this 
directly with getorf and sizeseq, my understanding is that sizeseq won't 
allow me to select the longest ORF for each input sequence. I can make 
the loop myself, but I won't unless it is not ?here somewhere in EMBOSS ;).
Cheers,
Herv?

On 12/06/2011 01:53 PM, Andres Pinzon wrote:
> Herve,
> Have you tried using "getorf" and then "sizeseq"?
> I think it will work. Then you could get the first sequence from the output.
>
> Best,
>
> On Tue, Dec 6, 2011 at 6:11 AM, Jon Ison<jison at ebi.ac.uk>  wrote:
>> A note of it is already on the SourceForge "Feature Requests" ...
>>
>> J:)
>>
>>
>>
>>> Hi Jon,
>>>
>>> That's exactly what would make me happy. Assuming it makes it easier for
>>> you if I formulate officially this request, where do I need to send the
>>> request?
>>>
>>> Herv?
>>>
>>> On 12/06/2011 12:00 PM, Jon Ison wrote:
>>>> Hi Herv?
>>>>
>>>> Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the
>>>> longest
>>>> ORF then that should be an easy enough option to add.
>>>>
>>>> Cheers
>>>>
>>>> Jon
>>>>
>>>>
>>>>> Hi,
>>>>> I have been using transeq and checktrans to find ORFs in DNA sequences.
>>>>> I have an question regarding the selection of the ORFs in case
>>>>> checktrans finds multiple ones in the result of transeq: I would like to
>>>>> select the longest one automatically (assuming it is the correct one).
>>>>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>>>>> library) that does this job?
>>>>> Cheers,
>>>>> Herv?
>>>>> _______________________________________________
>>>>> EMBOSS mailing list
>>>>> EMBOSS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>>
>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>
>
>


From andrespinzon at gmail.com  Tue Dec  6 09:19:39 2011
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Tue, 6 Dec 2011 09:19:39 -0500
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <4EDE249B.7080207@pasteur.fr>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
	<4EDDF75F.8020400@pasteur.fr>
	<48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>
	<CACmy5HD6hydbvfEtXo7Pxnp3-YsLDkqt5k1_hp1Q75PouhM3AQ@mail.gmail.com>
	<4EDE249B.7080207@pasteur.fr>
Message-ID: <CACmy5HAXK_rC9jehW7+vHfnepXE8+=h8m6tg-BYOaHFZe9H7Ew@mail.gmail.com>

D'accord ;)

Best

On Tue, Dec 6, 2011 at 9:20 AM, Herv? M?nager <hmenager at pasteur.fr> wrote:
> Hi Andres,
> From my point of view, it would do the job if I didn't have a _list_ of
> genes as an input: I hence need to input a list of genes and get as an
> output a list of the longest ORF computed for each gene. If I do this
> directly with getorf and sizeseq, my understanding is that sizeseq won't
> allow me to select the longest ORF for each input sequence. I can make the
> loop myself, but I won't unless it is not ?here somewhere in EMBOSS ;).
> Cheers,
> Herv?
>
>
> On 12/06/2011 01:53 PM, Andres Pinzon wrote:
>>
>> Herve,
>> Have you tried using "getorf" and then "sizeseq"?
>> I think it will work. Then you could get the first sequence from the
>> output.
>>
>> Best,
>>
>> On Tue, Dec 6, 2011 at 6:11 AM, Jon Ison<jison at ebi.ac.uk> ?wrote:
>>>
>>> A note of it is already on the SourceForge "Feature Requests" ...
>>>
>>> J:)
>>>
>>>
>>>
>>>> Hi Jon,
>>>>
>>>> That's exactly what would make me happy. Assuming it makes it easier for
>>>> you if I formulate officially this request, where do I need to send the
>>>> request?
>>>>
>>>> Herv?
>>>>
>>>> On 12/06/2011 12:00 PM, Jon Ison wrote:
>>>>>
>>>>> Hi Herv?
>>>>>
>>>>> Nothing in EMBOSS so far as I'm aware, but if all you want is for
>>>>> checktrans to report the
>>>>> longest
>>>>> ORF then that should be an easy enough option to add.
>>>>>
>>>>> Cheers
>>>>>
>>>>> Jon
>>>>>
>>>>>
>>>>>> Hi,
>>>>>> I have been using transeq and checktrans to find ORFs in DNA
>>>>>> sequences.
>>>>>> I have an question regarding the selection of the ORFs in case
>>>>>> checktrans finds multiple ones in the result of transeq: I would like
>>>>>> to
>>>>>> select the longest one automatically (assuming it is the correct one).
>>>>>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>>>>>> library) that does this job?
>>>>>> Cheers,
>>>>>> Herv?
>>>>>> _______________________________________________
>>>>>> EMBOSS mailing list
>>>>>> EMBOSS at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>>
>>
>>
>



-- 
Andr?s Pinz?n


From Scott.Markel at accelrys.com  Tue Dec  6 15:21:05 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Tue, 6 Dec 2011 12:21:05 -0800
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <4EDDD7D1.4030001@ebi.ac.uk>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783783@EXCH1-COLO.accelrys.net>
	<4EDDD7D1.4030001@ebi.ac.uk>
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702FA78386B@EXCH1-COLO.accelrys.net>

Peter,

Yes, what I generated for you was Windows-based, but we run EMBOSS on both Windows and Linux in Pipeline Pilot.

Regarding a patch, our next release is later in 2012, so whatever is more convenient for you regarding timing is fine with us.

Scott


-----Original Message-----
From: Peter Rice [mailto:pmr at ebi.ac.uk] 
Sent: Tuesday, 06 December 06 2011 12:53 AM
To: Scott Markel
Cc: emboss at lists.open-bio.org; Kristine Briedis
Subject: Re: HTML tag mismatch in acdtable output for fuzzpro

Dear Scott,

On 06/12/2011 00:35, Scott Markel wrote:
> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.

> And here are the three sets of tag mismatches in the HTML.  All involve an opening<th>  and a closing</td>.

Oops. Well spotted. Simple fix in ajax/acd/ajacd.c ... we have a new 
release due in January when our current funding ends, but will look to 
release a patch for you.

 From the version number, was this mEMBOSS you were using?

regards,

Peter Rice
EMBOSS Team




From Scott.Markel at accelrys.com  Tue Dec  6 15:21:18 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Tue, 6 Dec 2011 12:21:18 -0800
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <BD5A1F3D-0EE3-4B8E-9E54-947CCD8D2CCE@illinois.edu>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>
	<BD5A1F3D-0EE3-4B8E-9E54-947CCD8D2CCE@illinois.edu>
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702FA78386C@EXCH1-COLO.accelrys.net>

Chris,

I don't think so.  We certainly made changes to our BioPerl copy to work around the EMBOSS bug, but I don't think BioPerl needs to incorporate what we did (writing a little subroutine to fix the tags).  An EMBOSS fix takes care of our problem.

Scott


-----Original Message-----
From: Fields, Christopher J [mailto:cjfields at illinois.edu] 
Sent: Monday, 05 December 05 2011 6:04 PM
To: Scott Markel
Cc: emboss at lists.open-bio.org; Kristine Briedis
Subject: Re: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro

Scott, is this something that needs to be addressed on the bioperl end?

chris

On Dec 5, 2011, at 7:14 PM, Scott Markel wrote:

> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.
> 
> Here are EMBOSS command lines for embossversion and acdtable.
> 
>> embossversion
> Reports the current EMBOSS version number
> 6.4.0.2
> 
>> acdtable fuzzpro -help -verbose >& fuzzpro_6.4.0.html
> 
> And here are the three sets of tag mismatches in the HTML.  All involve an opening <th> and a closing </td>.
> 
> Lines 66-9:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-sequence" associated seqall qualifiers </td> </tr>
> 
> Lines 183-6:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-pattern" associated pattern qualifiers </td> </tr>
> 
> Lines 212-5:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-outfile" associated report qualifiers </td> </tr>
> 
> Scott
> 
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> San Diego, CA 92121                 fax:    +1 858 799 5222
> USA                                 web:    http://www.accelrys.com
> 
> http://www.linkedin.com/in/smarkel
> Secretary, Board of Directors:
>     International Society for Computational Biology
> Chair: ISCB Publications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
> 
> 
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss





From cjfields at illinois.edu  Tue Dec  6 17:00:52 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 6 Dec 2011 22:00:52 +0000
Subject: [EMBOSS] problem with EMBOSS configuration '--without x'
Message-ID: <68A7E0DA-660A-48CC-9646-4E3CD42C2367@illinois.edu>

Not sure when the next version is due out, but I thought this is worth mentioning in case someone else runs into it.  We had an odd issue with our local EMBOSS installation (6.4.0) on a RHEL VM which is likely a bug in the configuration step.  We were installing for use mainly with Galaxy, and didn't need X11 configuration, so we configured as follows:

./configure --prefix=/opt/local/Bio/EMBOSS --without-x

However, the installed binaries couldn't find the acd files or data; the only way to find them (as well as the data files) was to explicitly set EMBOSS_ACDROOT and EMBOSS_DATA.  Oddly, installing libx11-devel and removing the '--without-x' flag during configuration worked just fine, no need for default env variables or .embossrc files.

Anyone else run into this?

chris


Christopher Fields
Senior Research Scientist
National Center for Supercomputing Applications
Institute for Genomic Biology
University of Illinois Urbana-Champaign
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801



From cjfields at illinois.edu  Tue Dec  6 21:20:55 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 7 Dec 2011 02:20:55 +0000
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <5ACBA19439E77B43A06F4CAB897EC97702FA78386C@EXCH1-COLO.accelrys.net>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>
	<BD5A1F3D-0EE3-4B8E-9E54-947CCD8D2CCE@illinois.edu>
	<5ACBA19439E77B43A06F4CAB897EC97702FA78386C@EXCH1-COLO.accelrys.net>
Message-ID: <7A5DAABA-33BE-4D94-8224-2353D3C2B90F@illinois.edu>

Yeah, caught Peter's response on that.  Just wanted to make sure there isn't anything we need to do from our end :)

chris
 
On Dec 6, 2011, at 2:21 PM, Scott Markel wrote:

> Chris,
> 
> I don't think so.  We certainly made changes to our BioPerl copy to work around the EMBOSS bug, but I don't think BioPerl needs to incorporate what we did (writing a little subroutine to fix the tags).  An EMBOSS fix takes care of our problem.
> 
> Scott
> 
> 
> -----Original Message-----
> From: Fields, Christopher J [mailto:cjfields at illinois.edu] 
> Sent: Monday, 05 December 05 2011 6:04 PM
> To: Scott Markel
> Cc: emboss at lists.open-bio.org; Kristine Briedis
> Subject: Re: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
> 
> Scott, is this something that needs to be addressed on the bioperl end?
> 
> chris
> 
> On Dec 5, 2011, at 7:14 PM, Scott Markel wrote:
> 
>> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.
>> 
>> Here are EMBOSS command lines for embossversion and acdtable.
>> 
>>> embossversion
>> Reports the current EMBOSS version number
>> 6.4.0.2
>> 
>>> acdtable fuzzpro -help -verbose >& fuzzpro_6.4.0.html
>> 
>> And here are the three sets of tag mismatches in the HTML.  All involve an opening <th> and a closing </td>.
>> 
>> Lines 66-9:
>> 
>> <tr bgcolor="#FFFFCC">
>> <th align="left" colspan=5>"-sequence" associated seqall qualifiers </td> </tr>
>> 
>> Lines 183-6:
>> 
>> <tr bgcolor="#FFFFCC">
>> <th align="left" colspan=5>"-pattern" associated pattern qualifiers </td> </tr>
>> 
>> Lines 212-5:
>> 
>> <tr bgcolor="#FFFFCC">
>> <th align="left" colspan=5>"-outfile" associated report qualifiers </td> </tr>
>> 
>> Scott
>> 
>> Scott Markel, Ph.D.
>> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
>> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
>> San Diego, CA 92121                 fax:    +1 858 799 5222
>> USA                                 web:    http://www.accelrys.com
>> 
>> http://www.linkedin.com/in/smarkel
>> Secretary, Board of Directors:
>>    International Society for Computational Biology
>> Chair: ISCB Publications Committee
>> Associate Editor: PLoS Computational Biology
>> Editorial Board: Briefings in Bioinformatics
>> 
>> 
>> 
>> 
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
> 
> 
> 



From s.newslists at gmail.com  Sun Dec  4 10:25:56 2011
From: s.newslists at gmail.com (Stefan)
Date: Sun, 4 Dec 2011 11:25:56 +0100
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <4E159971.9070509@ebi.ac.uk>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
Message-ID: <CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>

2011/7/7 Peter Rice <pmr at ebi.ac.uk>:
> Very close to release date next week, so hard to do anything immediately.

Hello to the list,

are there any news in plasmid documentation and in-silico cloning with
EMBOSS? In the last month I was asked 4 times if this is possible with
EMBOSS. People like it to work with EMBOSS and want to do that things
also with this suite.

I would be happy to hear any progress.

Thanks
Stefan


From pmr at ebi.ac.uk  Sun Dec  4 20:22:12 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Sun, 04 Dec 2011 20:22:12 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
Message-ID: <4EDBD674.9050409@ebi.ac.uk>

On 04/12/2011 10:25, Stefan wrote:
> 2011/7/7 Peter Rice<pmr at ebi.ac.uk>:
>> Very close to release date next week, so hard to do anything immediately.
>
> are there any news in plasmid documentation and in-silico cloning with
> EMBOSS? In the last month I was asked 4 times if this is possible with
> EMBOSS. People like it to work with EMBOSS and want to do that things
> also with this suite.

Can you give us some examples of what you would like to see? Examples 
always help us to design new applicatons.

We still only have cirdna, mainly because we are limited by the plplot 
graphics library (and would welcome suggestions of other graphics 
libraries we could try).

We have extended the capabilities by creating input files from some 
other applications.

regards,

Peter Rice
EMBOSS team


From pmr at ebi.ac.uk  Mon Dec  5 09:26:00 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 05 Dec 2011 09:26:00 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <4EDC8BDA.30006@fmi.ch>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
	<4EDBD674.9050409@ebi.ac.uk> <4EDC8BDA.30006@fmi.ch>
Message-ID: <4EDC8E28.7090702@ebi.ac.uk>

On 12/05/2011 09:16 AM, Hans-Rudolf Hotz wrote:
> Thanks to the Galaxy framework, our lab scientist are using more and
> more EMBOSS tools. Now, it would be very handy if there was an EMBOSS
> drawing tool (even a very simple one) which takes an embl or genbank
> file as input and creates something "colorful". By default each Key or
> Qualifier is given a specific color and shape (eg 'arrow'). And you can
> change them as options.

Interesting suggestion. Can you send an example of what you would like 
to see?

You can use your favourite drawing tool if you like, but it is OK if you 
draw it in crayon, scan it and send the image :-)

regards,

Peter Rice
EMBOSS team


From hrh at fmi.ch  Mon Dec  5 09:16:10 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Mon, 5 Dec 2011 10:16:10 +0100
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <4EDBD674.9050409@ebi.ac.uk>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
	<4EDBD674.9050409@ebi.ac.uk>
Message-ID: <4EDC8BDA.30006@fmi.ch>



On 12/04/2011 09:22 PM, Peter Rice wrote:
> On 04/12/2011 10:25, Stefan wrote:
>> 2011/7/7 Peter Rice<pmr at ebi.ac.uk>:
>>> Very close to release date next week, so hard to do anything
>>> immediately.
>>
>> are there any news in plasmid documentation and in-silico cloning with
>> EMBOSS? In the last month I was asked 4 times if this is possible with
>> EMBOSS. People like it to work with EMBOSS and want to do that things
>> also with this suite.
>
> Can you give us some examples of what you would like to see? Examples
> always help us to design new applicatons.
>

Hi Peter and Stefan

Please allow me to jump in and tell you about our situation:

Our wet lab scientist use depending (which lab/university they are 
coming from) a combination of old commercial products (which we can 
still use thank to the perpetual licenses) and free/open source products 
like 'Serial Cloner', 'Ape', 'Gentle', etc

I constantly 'preach' how vital it is to make sure you safe each 
sequence/plasmid/etc not only in the tool specific format, but also in a 
text format like embl or genbank, where all the annotation is stored in 
the Feature Table

Thanks to the Galaxy framework, our lab scientist are using more and 
more EMBOSS tools. Now, it would be very handy if there was an EMBOSS 
drawing tool (even a very simple one) which takes an embl or genbank 
file as input and creates something "colorful". By default each Key or 
Qualifier is given a specific color and shape (eg 'arrow'). And you can 
change them as options.

I hope this works as a use case?


Regards, Hans



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland

> We still only have cirdna, mainly because we are limited by the plplot
> graphics library (and would welcome suggestions of other graphics
> libraries we could try).
>
> We have extended the capabilities by creating input files from some
> other applications.
>
> regards,
>
> Peter Rice
> EMBOSS team
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


From p.j.a.cock at googlemail.com  Mon Dec  5 10:08:59 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Dec 2011 10:08:59 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <4EDC8E28.7090702@ebi.ac.uk>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
	<4EDBD674.9050409@ebi.ac.uk> <4EDC8BDA.30006@fmi.ch>
	<4EDC8E28.7090702@ebi.ac.uk>
Message-ID: <CAKVJ-_7YeStqhNQjkOp0NW=qfD97QdH_WAh59wLSQuty-vWLGg@mail.gmail.com>

On Mon, Dec 5, 2011 at 9:26 AM, Peter Rice <pmr at ebi.ac.uk> wrote:
> On 12/05/2011 09:16 AM, Hans-Rudolf Hotz wrote:
>>
>> Thanks to the Galaxy framework, our lab scientist are using more and
>> more EMBOSS tools. Now, it would be very handy if there was an EMBOSS
>> drawing tool (even a very simple one) which takes an embl or genbank
>> file as input and creates something "colorful". By default each Key or
>> Qualifier is given a specific color and shape (eg 'arrow'). And you can
>> change them as options.
>
> Interesting suggestion. Can you send an example of what you
> would like to see?
>
> You can use your favourite drawing tool if you like, but it is OK if
> you draw it in crayon, scan it and send the image :-)
>

I use Biopython's GenomeDiagram for this sort of thing, which
internally uses a Python library called ReportLab which can
produce PDF, SVG, PNG, etc. Sadly I doubt that would be
suitable for EMBOSS which would really want a C library.

GenomeDiagram has the notion of tracks - which can be
useful for separating different types of features which would
otherwise overlap (e.g. gene/mRNA/CDS) and other tricks.
It also has some defaults about which feature qualifiers
to use as the feature name (e.g. gene, locustag).

I have considered writing a Galaxy tool to take an EMBL or
GenBank file and produce a picture, but haven't got round
to it yet.

Anyway, there may be some useful ideas for layout here
if nothing else.

Peter


From pmr at ebi.ac.uk  Mon Dec  5 10:19:41 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 05 Dec 2011 10:19:41 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <CAKVJ-_7YeStqhNQjkOp0NW=qfD97QdH_WAh59wLSQuty-vWLGg@mail.gmail.com>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
	<4EDBD674.9050409@ebi.ac.uk> <4EDC8BDA.30006@fmi.ch>
	<4EDC8E28.7090702@ebi.ac.uk>
	<CAKVJ-_7YeStqhNQjkOp0NW=qfD97QdH_WAh59wLSQuty-vWLGg@mail.gmail.com>
Message-ID: <4EDC9ABD.2020605@ebi.ac.uk>

On 12/05/2011 10:08 AM, Peter Cock wrote:
> I use Biopython's GenomeDiagram for this sort of thing, which
> internally uses a Python library called ReportLab which can
> produce PDF, SVG, PNG, etc. Sadly I doubt that would be
> suitable for EMBOSS which would really want a C library.
>
> GenomeDiagram has the notion of tracks - which can be
> useful for separating different types of features which would
> otherwise overlap (e.g. gene/mRNA/CDS) and other tricks.
> It also has some defaults about which feature qualifiers
> to use as the feature name (e.g. gene, locustag).

The EMBOSS solution to tracks would probably use the Sequence Ontology 
to define the tracks, and use features below some specified tag (or set 
of tags) for each track.

We can apply the same tracks to showfeat (the text display of features)

Tracks also simplify the issues of colours for features.

lindna has code for rendering features withg scaling and avoiding 
overlaps which we could also, I hope, reuse.

Maybe not for the next release (release date 15th January, but code 
freeze before Christmas) but we can provide applications for testing by 
anyone interested after the release.

regards,

Peter Rice
EMBOSS Team



From david.bauer at bayer.com  Mon Dec  5 09:38:34 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Mon, 5 Dec 2011 10:38:34 +0100
Subject: [EMBOSS] Plasmid drawing
Message-ID: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>

Hi Peter,

I think Stefan means not only the drawing of plasmid maps but the creation 
of new constructs in the computer before doing it at the bench.
This is a field where there are currently only commercial packages 
available like VectorNTI and Clone Manager (
http://www.scied.com/pr_cmpro.htm) etc.
Clone manager is there since the times of MS-DOS but the prices have 
increased substantially. They used to advertise the software with the 
slogan: "It costs only as much as a cloning kit for the lab" - which was 
in the range of 300,-USD.

The most important functions, which I think should be implement first are 
the cloning operations.
So e.g. 
- take plasmid1, open the multi cloning site with BamHI and EcoRI
- take plasmid2, cut out a fragment with BglII and EcoRI
- ligate the fragment from plasmid2 into plasmid1
        (BamHI and BglII have compatible ends which can be ligated, so an 
algorithm is needed to check this)
- draw a map of the newly created plasmid3
This is a rather simple example.
There can be more complex procedures like Klenow fill in (blunt end 
ligation of incompatible restriction sites) or the use of more than 2 
fragments in one ligation.

I think most of the functions needed for this are already present in 
EMBOSS.
It shouldn't be so complicated to create an application which uses 
functions from restrict, cutseq, pasteseq to accomplish the above 
mentioned task.
Although it's probably not so trivial to make this happen before the 
release next week ;-)

Cheers,
David.




Peter Rice <pmr at ebi.ac.uk> 
Gesendet von: emboss-bounces at lists.open-bio.org
04/12/2011 21:22

An
Stefan <s.newslists at gmail.com>
Kopie
emboss at lists.open-bio.org
Thema
Re: [EMBOSS] Plasmid drawing






On 04/12/2011 10:25, Stefan wrote:
> 2011/7/7 Peter Rice<pmr at ebi.ac.uk>:
>> Very close to release date next week, so hard to do anything 
immediately.
>
> are there any news in plasmid documentation and in-silico cloning with
> EMBOSS? In the last month I was asked 4 times if this is possible with
> EMBOSS. People like it to work with EMBOSS and want to do that things
> also with this suite.

Can you give us some examples of what you would like to see? Examples 
always help us to design new applicatons.

We still only have cirdna, mainly because we are limited by the plplot 
graphics library (and would welcome suggestions of other graphics 
libraries we could try).

We have extended the capabilities by creating input files from some 
other applications.

regards,

Peter Rice
EMBOSS team
_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss



From s.newslists at gmail.com  Mon Dec  5 10:44:34 2011
From: s.newslists at gmail.com (Stefan)
Date: Mon, 5 Dec 2011 11:44:34 +0100
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>
References: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>
Message-ID: <CAECtV7M+PWO+_cgV8BH0cdYEu0Kx9yTzhg3NVbJT_d2KC9=_PA@mail.gmail.com>

> I think Stefan means not only the drawing of plasmid maps but the creation of new constructs in the computer before doing it at the bench.
What David wrote is exactly what I wanted to explain with "in-silico cloning".
With plasmid documentation I meant that it is possible to draw
aplasmid with features and restriction sites.
Thanks


From pmr at ebi.ac.uk  Mon Dec  5 13:23:23 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 05 Dec 2011 13:23:23 +0000
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <CB027D1E.5D88%hrh@fmi.ch>
References: <CB027D1E.5D88%hrh@fmi.ch>
Message-ID: <4EDCC5CB.2090402@ebi.ac.uk>

On 05/12/2011 12:52, Hotz, Hans-Rudolf wrote:

> "cirdna" and "lindna" are nice and do their job most of the time. In my
> view, the problem is the input file format. Maybe a converter from
> embl/genbank to *.crip or *.linp would be a good start? Or adding the those
> formats to the output options of seqret?

We do already support "draw" an a report output format.

If we add it as a feature output format you can use featcopy (or seqret 
-feat) to create a cirdna or lindna input file.

We can then work on the feature format to add extra information by 
feature type.

We could also add an application to merge a set of feature inputs so you 
could combine genbank/embl files with restriction map output, then use 
the results as input.

I will see what I can do for the next release.

Thanks for the very helpful suggestions

Peter Rice
EMBOSS Team


From marko at cryst.bioc.cam.ac.uk  Mon Dec  5 13:10:06 2011
From: marko at cryst.bioc.cam.ac.uk (Marko Hyvonen)
Date: Mon, 5 Dec 2011 13:10:06 +0000 (GMT)
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>
References: <OFFBCBE961.0A95F47E-ONC125795D.0034DF22-C125795D.0034F813@bayer.de>
Message-ID: <alpine.LNX.2.00.1112051300590.5959@mackerel.bioc.cam.ac.uk>



I would find this kind of in silico cloning great addition to EMBOSS.

As an example of (a free?) drawing program for plasmids, I use PlasMapper 
(http://wishart.biology.ualberta.ca/PlasMapper/ , source code is at least 
available on the site). Here is an example I made from their own selection 
of plasmids (hopefully valid link for a while still):
  http://wishart.biology.ualberta.ca/PlasMapper/jsp/displayPlasmidMap.jsp?fileName=plasMap26_1323082022185.png&fileFormat=png

I like the fact that it includes a number of predefined features in 
plasmids as built-ins, so that you only need to include the "unique" 
features in your own plasmids (and I am sure the set of built-ins could be 
expanded much further). Outputs svg too, which is brilliant for editing 
later on.

Marko


On Mon, 5 Dec 2011, david.bauer at bayer.com wrote:

> Hi Peter,
>
> I think Stefan means not only the drawing of plasmid maps but the creation
> of new constructs in the computer before doing it at the bench.
> This is a field where there are currently only commercial packages
> available like VectorNTI and Clone Manager (
> http://www.scied.com/pr_cmpro.htm) etc.
> Clone manager is there since the times of MS-DOS but the prices have
> increased substantially. They used to advertise the software with the
> slogan: "It costs only as much as a cloning kit for the lab" - which was
> in the range of 300,-USD.
>
> The most important functions, which I think should be implement first are
> the cloning operations.
> So e.g.
> - take plasmid1, open the multi cloning site with BamHI and EcoRI
> - take plasmid2, cut out a fragment with BglII and EcoRI
> - ligate the fragment from plasmid2 into plasmid1
>        (BamHI and BglII have compatible ends which can be ligated, so an
> algorithm is needed to check this)
> - draw a map of the newly created plasmid3
> This is a rather simple example.
> There can be more complex procedures like Klenow fill in (blunt end
> ligation of incompatible restriction sites) or the use of more than 2
> fragments in one ligation.
>
> I think most of the functions needed for this are already present in
> EMBOSS.
> It shouldn't be so complicated to create an application which uses
> functions from restrict, cutseq, pasteseq to accomplish the above
> mentioned task.
> Although it's probably not so trivial to make this happen before the
> release next week ;-)
>
> Cheers,
> David.
>
>
>
>
> Peter Rice <pmr at ebi.ac.uk>
> Gesendet von: emboss-bounces at lists.open-bio.org
> 04/12/2011 21:22
>
> An
> Stefan <s.newslists at gmail.com>
> Kopie
> emboss at lists.open-bio.org
> Thema
> Re: [EMBOSS] Plasmid drawing
>
>
>
>
>
>
> On 04/12/2011 10:25, Stefan wrote:
>> 2011/7/7 Peter Rice<pmr at ebi.ac.uk>:
>>> Very close to release date next week, so hard to do anything
> immediately.
>>
>> are there any news in plasmid documentation and in-silico cloning with
>> EMBOSS? In the last month I was asked 4 times if this is possible with
>> EMBOSS. People like it to work with EMBOSS and want to do that things
>> also with this suite.
>
> Can you give us some examples of what you would like to see? Examples
> always help us to design new applicatons.
>
> We still only have cirdna, mainly because we are limited by the plplot
> graphics library (and would welcome suggestions of other graphics
> libraries we could try).
>
> We have extended the capabilities by creating input files from some
> other applications.
>
> regards,
>
> Peter Rice
> EMBOSS team
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>


  _____________________________________

  Marko Hyvonen
  Department of Biochemistry, University of Cambridge
  marko at cryst.bioc.cam.ac.uk
  http://www-cryst.bioc.cam.ac.uk/groups/hyvonen
  tel:    +44-(0)1223-766 044
  mobile: +44-(0)7796-174 877
  fax:    +44-(0)1223-766 002
  --------------------------------------


From hmenager at pasteur.fr  Mon Dec  5 16:14:20 2011
From: hmenager at pasteur.fr (=?ISO-8859-1?Q?Herv=E9_M=E9nager?=)
Date: Mon, 05 Dec 2011 17:14:20 +0100
Subject: [EMBOSS] ORF selection with EMBOSS
Message-ID: <4EDCEDDC.3020200@pasteur.fr>

Hi,
I have been using transeq and checktrans to find ORFs in DNA sequences. 
I have an question regarding the selection of the ORFs in case 
checktrans finds multiple ones in the result of transeq: I would like to 
select the longest one automatically (assuming it is the correct one). 
Is there any existing tool in EMBOSS (or alternatively in any Bio* 
library) that does this job?
Cheers,
Herv?


From mathog at caltech.edu  Mon Dec  5 16:35:31 2011
From: mathog at caltech.edu (mathog)
Date: Mon, 05 Dec 2011 08:35:31 -0800
Subject: [EMBOSS] Plasmid drawing
In-Reply-To: <CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
References: <CAOhDcVx+yZPGE4-zEHb8GeMd5eyLg1GX+V2CrHgWVjrtshSHeA@mail.gmail.com>
	<4E159971.9070509@ebi.ac.uk>
	<CAECtV7OS491MTAAaqmx5eP3HsD4HocMKz--tDU=D-uAzHyjawQ@mail.gmail.com>
Message-ID: <a5f593a8b406dc04b53acc6ffc899ea7@saf.bio.caltech.edu>

On Sun, 4 Dec 2011 11:25:56 +0100, Stefan wrote:

> are there any news in plasmid documentation and in-silico cloning 
> with
> EMBOSS?

Pierre Lindenbaum wrote a nice little program called "cloneit" for 
figuring out cloning
strategies.  That is, specifically what series of reactions to use to 
insert a particular
piece of DNA into a vector.  Not sure if that is what you mean by 
"in-silico cloning" or not. There is
a separate cgi version for web use.  Here is the paper:

http://www.ncbi.nlm.nih.gov/pubmed/9682060?dopt=Abstract

The original distribution site is long since off line, but the code 
says that it may
be redistributed (and incorporated in noncommercial software, but see 
the exact wording
for details.)  Anyway, if anybody wants to have a look, I packed up our 
copies and put
them here:

http://saf.bio.caltech.edu/pub/software/molbio/cloneit.tar.gz
http://saf.bio.caltech.edu/pub/software/molbio/cloneitcgi.tar.gz

This is not a graphics program, it is a reaction planning program.

As for the graphical output of plasmid diagrams, historically none of 
the drawing programs
does exactly what the end users want.  (These get closer and closer, 
but never quite cover
all the bases).  For that reason it is really important that the 
graphics driver be able to
output to an object format that can then be imported into a drawing 
program and edited there.
Modifying an image never turns out as nicely.  When going to object 
formats it is key that
text remain text and not be converted into line segments or
paths. Users get really frustrated when they can't edit labels or 
change fonts or font sizes.
Locally we have a hacked up GCG driver that emits cgm format for the 
GCG drawing programs.
Nowadays going to SVG would make more sense.

While it is sometimes possible to read PDF back into a drawing program 
like inkscape, text imported
that way is very hit and miss, mostly miss.  Often it comes through 
with each
letter as a separate text object, which is no fun at all to work with.  
Other times it will come in with
each letter separately kerned, and when that kerning is removed, the 
text jumps all over the place in
unpredictable ways.  Why would you remove the kerning?  Because there 
is another bug/limitation
in inkscape where kerned text is automatically converted to images when 
exporting to emf or wmf format,
as when trying to move that image into a powerpoint document.  Moving 
rotated text between various
programs is the most unreliable operation, as far as I can tell.  For 
instance, I have never found
a way to get text which runs at an angle other than 0 degrees from 
inskcape into powerpoint with that
angle intact.  The text comes through, but the angle is lost.

Regards,


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech


From Scott.Markel at accelrys.com  Tue Dec  6 01:14:19 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Mon, 5 Dec 2011 17:14:19 -0800
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>

We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.

Here are EMBOSS command lines for embossversion and acdtable.

> embossversion
Reports the current EMBOSS version number
6.4.0.2

> acdtable fuzzpro -help -verbose >& fuzzpro_6.4.0.html

And here are the three sets of tag mismatches in the HTML.  All involve an opening <th> and a closing </td>.

Lines 66-9:

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>"-sequence" associated seqall qualifiers </td> </tr>

Lines 183-6:

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>"-pattern" associated pattern qualifiers </td> </tr>

Lines 212-5:

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>"-outfile" associated report qualifiers </td> </tr>

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect? email:? smarkel at accelrys.com
Accelrys (Pipeline Pilot R&D)?????? mobile: +1 858 205 3653
10188 Telesis Court, Suite 100????? voice:? +1 858 799 5603
San Diego, CA 92121???????????????? fax:??? +1 858 799 5222
USA???????????????????????????????? web:??? http://www.accelrys.com

http://www.linkedin.com/in/smarkel
Secretary, Board of Directors:
??? International Society for Computational Biology
Chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics






From cjfields at illinois.edu  Tue Dec  6 02:03:35 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 6 Dec 2011 02:03:35 +0000
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>
Message-ID: <BD5A1F3D-0EE3-4B8E-9E54-947CCD8D2CCE@illinois.edu>

Scott, is this something that needs to be addressed on the bioperl end?

chris

On Dec 5, 2011, at 7:14 PM, Scott Markel wrote:

> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.
> 
> Here are EMBOSS command lines for embossversion and acdtable.
> 
>> embossversion
> Reports the current EMBOSS version number
> 6.4.0.2
> 
>> acdtable fuzzpro -help -verbose >& fuzzpro_6.4.0.html
> 
> And here are the three sets of tag mismatches in the HTML.  All involve an opening <th> and a closing </td>.
> 
> Lines 66-9:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-sequence" associated seqall qualifiers </td> </tr>
> 
> Lines 183-6:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-pattern" associated pattern qualifiers </td> </tr>
> 
> Lines 212-5:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-outfile" associated report qualifiers </td> </tr>
> 
> Scott
> 
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> San Diego, CA 92121                 fax:    +1 858 799 5222
> USA                                 web:    http://www.accelrys.com
> 
> http://www.linkedin.com/in/smarkel
> Secretary, Board of Directors:
>     International Society for Computational Biology
> Chair: ISCB Publications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
> 
> 
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss




From pandey.gaurav at gmail.com  Tue Dec  6 04:07:10 2011
From: pandey.gaurav at gmail.com (Gaurav Pandey)
Date: Mon, 5 Dec 2011 23:07:10 -0500
Subject: [EMBOSS] Research opportunities in systems biology at Mt. Sinai
	School of Medicine
Message-ID: <CAMqOHCw34+o7iWwW_RZ3HyhY013WP=iiSkvO9nqvyrQoqH4=rQ@mail.gmail.com>

Please forward this announcement to potential applicants if it is not
directly applicable to you. Apologies for cross-posting.



---------------------------



The Institute for Genomics and Multi-scale Biology (multiscale.mssm.edu) at
the Mount Sinai School of Medicine (www.mssm.edu) in New York City is
seeking applications from enthusiastic and capable researchers for
positions at Ph.D., postdoc and staff level. The Institute is the hub of
genomics research at Mount Sinai, collaborating with13 other
disease-oriented and core-technology-based institutes, and aims to
translate genomics-based science into actionable medical knowledge. The
Institute's faculty members have expertise in a wide range of areas such as
machine learning, biostatistics, genetics, genomics, sequencing technology,
data science, and high-performance computing (HPC).



We wish to recruit capable and motivated graduate students, post-doctoral
associates, and research staff members. Please look at the detailed
announcement at the end of this email providing information on specific
requirements for these positions. PhD and MD/PhD applicants should consult
the requirements of the Graduate School at Mount Sinai (
http://www.mssm.edu/education/graduate-school) for application and
potential admission. Others should send their requisite application
material (see below) to multiscale.biology at mssm.edu. For more information,
visit the Institute's website (multiscale.mssm.edu) and/or email
multiscale.biology at mssm.edu.



-------------------------------

The Multiscale Institute is actively recruiting graduate students,
post-doctoral scholars and technical staff interested in working on
challenging and important problems in computational systems biology,
especially with a focus on translating this work to the medical domain.

Prospective Students

If you are a prospective MD (
http://www.mssm.edu/education/medical-education/programs/md-program), Ph.D.
or MD/Ph.D. (http://www.mssm.edu/education/graduate-school) student, the
Multiscale Institute provides a cutting-edge research environment, strong
mentorship and comprehensive training in computational biology. Please
check out the various degree programs within the Mount Sinai School of
Medicine, and for Ph.D. students, the Genetics and Genomics Training Area
(http://www.mssm.edu/education/graduate-school/degrees-and-programs/phd-program/multidisciplinary-training-areas/genetics-and-genomic-sciences)<file://localhost/about/blank>in
particular, for more information. Alternatively, contact us directly
at
multiscale.biology at mssm.edu for information.

The Multiscale Institute faculty members have backgrounds in Computer
Science, Engineering, Statistics, Mathematics, Physics, Genetics, Molecular
Biology, and related disciplines, and are looking for students from all of
those fields. The essential requirement is an interest in and capability of
thinking about real-world problems in quantitative terms. Additional
desired (but not essential) characteristics will be (1) a background in
biology, acquired through courses and/or research work and/or (2)
experience with data-intensive real-world problems (from any domain) and/or
(3) experience with programming.

If you are not yet applying to graduate school, we recommend you to check
out SURP (
http://www.mssm.edu/education/graduate-school/degrees-and-programs/summer-undergraduate-research-program),
the Summer Undergraduate Research Program at Mount Sinai.

Prospective Post-doctoral Scholars

At the Multiscale Institute, you will have a chance to work with world
class scientists and engineers tackling important and highly visible
problems in computational biology, with an emphasis on translating such
work into the medical domain. Some example targets of the Institute are
identifying actionable biomarkers and therapeutics for complex human
diseases.

Candidates should have a recent PhD and/or MD degree in a science,
technology, engineering or medical field, and discipline and high
motivation to pursue independent research in computational biology.
Applicants are expected to have a solid background in programming and
computational techniques, with a working knowledge of molecular biology and
genetics being highly desirable. To apply, send a CV, a research statement
and contact information for three referees to the
multiscale.biology at mssm.edu. More information about postdoctoral training
at Mt. Sinai can be found at the Office of Postdoctoral Affairs (
http://www.mssm.edu/education/postdoctoral-training).

Technical Staff

We are looking for engineers and scientists to help Institute researchers
extract clinical insight from petabyte-scale data sets. The ideal candidate
will be comfortable in an academic environment, and will bring energy and
creativity to the Institute?s work. In particular, the applicant is
expected to have substantial experience working with big data and its
associated infrastructure, including data retrieval from a variety of
data-stores, statistics with R/C++/Java etc., and visualization for the web
and print. A biology background is desired, but not required; we are
primarily looking for people with strong data analysis and software
engineering skills. To apply, send your resume to
multiscale.biology at mssm.edu



-- 
Gaurav Pandey, Ph.D.
Assistant Professor
Department of Genetics and Genomic Sciences
Mount Sinai School of Medicine, New York City
http://www.mssm.edu/profiles/gaurav-pandey



From pmr at ebi.ac.uk  Tue Dec  6 08:52:33 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 06 Dec 2011 08:52:33 +0000
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <5ACBA19439E77B43A06F4CAB897EC97702FA783783@EXCH1-COLO.accelrys.net>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783783@EXCH1-COLO.accelrys.net>
Message-ID: <4EDDD7D1.4030001@ebi.ac.uk>

Dear Scott,

On 06/12/2011 00:35, Scott Markel wrote:
> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.

> And here are the three sets of tag mismatches in the HTML.  All involve an opening<th>  and a closing</td>.

Oops. Well spotted. Simple fix in ajax/acd/ajacd.c ... we have a new 
release due in January when our current funding ends, but will look to 
release a patch for you.

 From the version number, was this mEMBOSS you were using?

regards,

Peter Rice
EMBOSS Team


From jison at ebi.ac.uk  Tue Dec  6 11:00:15 2011
From: jison at ebi.ac.uk (Jon Ison)
Date: Tue, 6 Dec 2011 11:00:15 -0000 (UTC)
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <4EDCEDDC.3020200@pasteur.fr>
References: <4EDCEDDC.3020200@pasteur.fr>
Message-ID: <36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>

Hi Herv?

Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the longest
ORF then that should be an easy enough option to add.

Cheers

Jon


> Hi,
> I have been using transeq and checktrans to find ORFs in DNA sequences.
> I have an question regarding the selection of the ORFs in case
> checktrans finds multiple ones in the result of transeq: I would like to
> select the longest one automatically (assuming it is the correct one).
> Is there any existing tool in EMBOSS (or alternatively in any Bio*
> library) that does this job?
> Cheers,
> Herv?
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From hmenager at pasteur.fr  Tue Dec  6 11:07:11 2011
From: hmenager at pasteur.fr (=?ISO-8859-1?Q?Herv=E9_M=E9nager?=)
Date: Tue, 06 Dec 2011 12:07:11 +0100
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
Message-ID: <4EDDF75F.8020400@pasteur.fr>

Hi Jon,

That's exactly what would make me happy. Assuming it makes it easier for 
you if I formulate officially this request, where do I need to send the 
request?

Herv?

On 12/06/2011 12:00 PM, Jon Ison wrote:
> Hi Herv?
>
> Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the longest
> ORF then that should be an easy enough option to add.
>
> Cheers
>
> Jon
>
>
>> Hi,
>> I have been using transeq and checktrans to find ORFs in DNA sequences.
>> I have an question regarding the selection of the ORFs in case
>> checktrans finds multiple ones in the result of transeq: I would like to
>> select the longest one automatically (assuming it is the correct one).
>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>> library) that does this job?
>> Cheers,
>> Herv?
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>



From jison at ebi.ac.uk  Tue Dec  6 11:11:01 2011
From: jison at ebi.ac.uk (Jon Ison)
Date: Tue, 6 Dec 2011 11:11:01 -0000 (UTC)
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <4EDDF75F.8020400@pasteur.fr>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
	<4EDDF75F.8020400@pasteur.fr>
Message-ID: <48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>

A note of it is already on the SourceForge "Feature Requests" ...

J:)



> Hi Jon,
>
> That's exactly what would make me happy. Assuming it makes it easier for
> you if I formulate officially this request, where do I need to send the
> request?
>
> Herv?
>
> On 12/06/2011 12:00 PM, Jon Ison wrote:
>> Hi Herv?
>>
>> Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the
>> longest
>> ORF then that should be an easy enough option to add.
>>
>> Cheers
>>
>> Jon
>>
>>
>>> Hi,
>>> I have been using transeq and checktrans to find ORFs in DNA sequences.
>>> I have an question regarding the selection of the ORFs in case
>>> checktrans finds multiple ones in the result of transeq: I would like to
>>> select the longest one automatically (assuming it is the correct one).
>>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>>> library) that does this job?
>>> Cheers,
>>> Herv?
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>
>>
>




From andrespinzon at gmail.com  Tue Dec  6 12:53:36 2011
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Tue, 6 Dec 2011 07:53:36 -0500
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
	<4EDDF75F.8020400@pasteur.fr>
	<48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>
Message-ID: <CACmy5HD6hydbvfEtXo7Pxnp3-YsLDkqt5k1_hp1Q75PouhM3AQ@mail.gmail.com>

Herve,
Have you tried using "getorf" and then "sizeseq"?
I think it will work. Then you could get the first sequence from the output.

Best,

On Tue, Dec 6, 2011 at 6:11 AM, Jon Ison <jison at ebi.ac.uk> wrote:
> A note of it is already on the SourceForge "Feature Requests" ...
>
> J:)
>
>
>
>> Hi Jon,
>>
>> That's exactly what would make me happy. Assuming it makes it easier for
>> you if I formulate officially this request, where do I need to send the
>> request?
>>
>> Herv?
>>
>> On 12/06/2011 12:00 PM, Jon Ison wrote:
>>> Hi Herv?
>>>
>>> Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the
>>> longest
>>> ORF then that should be an easy enough option to add.
>>>
>>> Cheers
>>>
>>> Jon
>>>
>>>
>>>> Hi,
>>>> I have been using transeq and checktrans to find ORFs in DNA sequences.
>>>> I have an question regarding the selection of the ORFs in case
>>>> checktrans finds multiple ones in the result of transeq: I would like to
>>>> select the longest one automatically (assuming it is the correct one).
>>>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>>>> library) that does this job?
>>>> Cheers,
>>>> Herv?
>>>> _______________________________________________
>>>> EMBOSS mailing list
>>>> EMBOSS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>
>>>
>>>
>>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



-- 
Andr?s Pinz?n



From hmenager at pasteur.fr  Tue Dec  6 14:20:11 2011
From: hmenager at pasteur.fr (=?UTF-8?B?SGVydsOpIE3DqW5hZ2Vy?=)
Date: Tue, 06 Dec 2011 15:20:11 +0100
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <CACmy5HD6hydbvfEtXo7Pxnp3-YsLDkqt5k1_hp1Q75PouhM3AQ@mail.gmail.com>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
	<4EDDF75F.8020400@pasteur.fr>
	<48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>
	<CACmy5HD6hydbvfEtXo7Pxnp3-YsLDkqt5k1_hp1Q75PouhM3AQ@mail.gmail.com>
Message-ID: <4EDE249B.7080207@pasteur.fr>

Hi Andres,
 From my point of view, it would do the job if I didn't have a _list_ of 
genes as an input: I hence need to input a list of genes and get as an 
output a list of the longest ORF computed for each gene. If I do this 
directly with getorf and sizeseq, my understanding is that sizeseq won't 
allow me to select the longest ORF for each input sequence. I can make 
the loop myself, but I won't unless it is not ?here somewhere in EMBOSS ;).
Cheers,
Herv?

On 12/06/2011 01:53 PM, Andres Pinzon wrote:
> Herve,
> Have you tried using "getorf" and then "sizeseq"?
> I think it will work. Then you could get the first sequence from the output.
>
> Best,
>
> On Tue, Dec 6, 2011 at 6:11 AM, Jon Ison<jison at ebi.ac.uk>  wrote:
>> A note of it is already on the SourceForge "Feature Requests" ...
>>
>> J:)
>>
>>
>>
>>> Hi Jon,
>>>
>>> That's exactly what would make me happy. Assuming it makes it easier for
>>> you if I formulate officially this request, where do I need to send the
>>> request?
>>>
>>> Herv?
>>>
>>> On 12/06/2011 12:00 PM, Jon Ison wrote:
>>>> Hi Herv?
>>>>
>>>> Nothing in EMBOSS so far as I'm aware, but if all you want is for checktrans to report the
>>>> longest
>>>> ORF then that should be an easy enough option to add.
>>>>
>>>> Cheers
>>>>
>>>> Jon
>>>>
>>>>
>>>>> Hi,
>>>>> I have been using transeq and checktrans to find ORFs in DNA sequences.
>>>>> I have an question regarding the selection of the ORFs in case
>>>>> checktrans finds multiple ones in the result of transeq: I would like to
>>>>> select the longest one automatically (assuming it is the correct one).
>>>>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>>>>> library) that does this job?
>>>>> Cheers,
>>>>> Herv?
>>>>> _______________________________________________
>>>>> EMBOSS mailing list
>>>>> EMBOSS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>>
>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>
>
>



From andrespinzon at gmail.com  Tue Dec  6 14:19:39 2011
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Tue, 6 Dec 2011 09:19:39 -0500
Subject: [EMBOSS] ORF selection with EMBOSS
In-Reply-To: <4EDE249B.7080207@pasteur.fr>
References: <4EDCEDDC.3020200@pasteur.fr>
	<36253.172.22.100.208.1323169215.squirrel@webmail.ebi.ac.uk>
	<4EDDF75F.8020400@pasteur.fr>
	<48987.172.22.100.208.1323169861.squirrel@webmail.ebi.ac.uk>
	<CACmy5HD6hydbvfEtXo7Pxnp3-YsLDkqt5k1_hp1Q75PouhM3AQ@mail.gmail.com>
	<4EDE249B.7080207@pasteur.fr>
Message-ID: <CACmy5HAXK_rC9jehW7+vHfnepXE8+=h8m6tg-BYOaHFZe9H7Ew@mail.gmail.com>

D'accord ;)

Best

On Tue, Dec 6, 2011 at 9:20 AM, Herv? M?nager <hmenager at pasteur.fr> wrote:
> Hi Andres,
> From my point of view, it would do the job if I didn't have a _list_ of
> genes as an input: I hence need to input a list of genes and get as an
> output a list of the longest ORF computed for each gene. If I do this
> directly with getorf and sizeseq, my understanding is that sizeseq won't
> allow me to select the longest ORF for each input sequence. I can make the
> loop myself, but I won't unless it is not ?here somewhere in EMBOSS ;).
> Cheers,
> Herv?
>
>
> On 12/06/2011 01:53 PM, Andres Pinzon wrote:
>>
>> Herve,
>> Have you tried using "getorf" and then "sizeseq"?
>> I think it will work. Then you could get the first sequence from the
>> output.
>>
>> Best,
>>
>> On Tue, Dec 6, 2011 at 6:11 AM, Jon Ison<jison at ebi.ac.uk> ?wrote:
>>>
>>> A note of it is already on the SourceForge "Feature Requests" ...
>>>
>>> J:)
>>>
>>>
>>>
>>>> Hi Jon,
>>>>
>>>> That's exactly what would make me happy. Assuming it makes it easier for
>>>> you if I formulate officially this request, where do I need to send the
>>>> request?
>>>>
>>>> Herv?
>>>>
>>>> On 12/06/2011 12:00 PM, Jon Ison wrote:
>>>>>
>>>>> Hi Herv?
>>>>>
>>>>> Nothing in EMBOSS so far as I'm aware, but if all you want is for
>>>>> checktrans to report the
>>>>> longest
>>>>> ORF then that should be an easy enough option to add.
>>>>>
>>>>> Cheers
>>>>>
>>>>> Jon
>>>>>
>>>>>
>>>>>> Hi,
>>>>>> I have been using transeq and checktrans to find ORFs in DNA
>>>>>> sequences.
>>>>>> I have an question regarding the selection of the ORFs in case
>>>>>> checktrans finds multiple ones in the result of transeq: I would like
>>>>>> to
>>>>>> select the longest one automatically (assuming it is the correct one).
>>>>>> Is there any existing tool in EMBOSS (or alternatively in any Bio*
>>>>>> library) that does this job?
>>>>>> Cheers,
>>>>>> Herv?
>>>>>> _______________________________________________
>>>>>> EMBOSS mailing list
>>>>>> EMBOSS at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>>
>>
>>
>



-- 
Andr?s Pinz?n



From Scott.Markel at accelrys.com  Tue Dec  6 20:21:05 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Tue, 6 Dec 2011 12:21:05 -0800
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <4EDDD7D1.4030001@ebi.ac.uk>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783783@EXCH1-COLO.accelrys.net>
	<4EDDD7D1.4030001@ebi.ac.uk>
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702FA78386B@EXCH1-COLO.accelrys.net>

Peter,

Yes, what I generated for you was Windows-based, but we run EMBOSS on both Windows and Linux in Pipeline Pilot.

Regarding a patch, our next release is later in 2012, so whatever is more convenient for you regarding timing is fine with us.

Scott


-----Original Message-----
From: Peter Rice [mailto:pmr at ebi.ac.uk] 
Sent: Tuesday, 06 December 06 2011 12:53 AM
To: Scott Markel
Cc: emboss at lists.open-bio.org; Kristine Briedis
Subject: Re: HTML tag mismatch in acdtable output for fuzzpro

Dear Scott,

On 06/12/2011 00:35, Scott Markel wrote:
> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.

> And here are the three sets of tag mismatches in the HTML.  All involve an opening<th>  and a closing</td>.

Oops. Well spotted. Simple fix in ajax/acd/ajacd.c ... we have a new 
release due in January when our current funding ends, but will look to 
release a patch for you.

 From the version number, was this mEMBOSS you were using?

regards,

Peter Rice
EMBOSS Team





From Scott.Markel at accelrys.com  Tue Dec  6 20:21:18 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Tue, 6 Dec 2011 12:21:18 -0800
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <BD5A1F3D-0EE3-4B8E-9E54-947CCD8D2CCE@illinois.edu>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>
	<BD5A1F3D-0EE3-4B8E-9E54-947CCD8D2CCE@illinois.edu>
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702FA78386C@EXCH1-COLO.accelrys.net>

Chris,

I don't think so.  We certainly made changes to our BioPerl copy to work around the EMBOSS bug, but I don't think BioPerl needs to incorporate what we did (writing a little subroutine to fix the tags).  An EMBOSS fix takes care of our problem.

Scott


-----Original Message-----
From: Fields, Christopher J [mailto:cjfields at illinois.edu] 
Sent: Monday, 05 December 05 2011 6:04 PM
To: Scott Markel
Cc: emboss at lists.open-bio.org; Kristine Briedis
Subject: Re: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro

Scott, is this something that needs to be addressed on the bioperl end?

chris

On Dec 5, 2011, at 7:14 PM, Scott Markel wrote:

> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.
> 
> Here are EMBOSS command lines for embossversion and acdtable.
> 
>> embossversion
> Reports the current EMBOSS version number
> 6.4.0.2
> 
>> acdtable fuzzpro -help -verbose >& fuzzpro_6.4.0.html
> 
> And here are the three sets of tag mismatches in the HTML.  All involve an opening <th> and a closing </td>.
> 
> Lines 66-9:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-sequence" associated seqall qualifiers </td> </tr>
> 
> Lines 183-6:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-pattern" associated pattern qualifiers </td> </tr>
> 
> Lines 212-5:
> 
> <tr bgcolor="#FFFFCC">
> <th align="left" colspan=5>"-outfile" associated report qualifiers </td> </tr>
> 
> Scott
> 
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> San Diego, CA 92121                 fax:    +1 858 799 5222
> USA                                 web:    http://www.accelrys.com
> 
> http://www.linkedin.com/in/smarkel
> Secretary, Board of Directors:
>     International Society for Computational Biology
> Chair: ISCB Publications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
> 
> 
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss






From cjfields at illinois.edu  Tue Dec  6 22:00:52 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 6 Dec 2011 22:00:52 +0000
Subject: [EMBOSS] problem with EMBOSS configuration '--without x'
Message-ID: <68A7E0DA-660A-48CC-9646-4E3CD42C2367@illinois.edu>

Not sure when the next version is due out, but I thought this is worth mentioning in case someone else runs into it.  We had an odd issue with our local EMBOSS installation (6.4.0) on a RHEL VM which is likely a bug in the configuration step.  We were installing for use mainly with Galaxy, and didn't need X11 configuration, so we configured as follows:

./configure --prefix=/opt/local/Bio/EMBOSS --without-x

However, the installed binaries couldn't find the acd files or data; the only way to find them (as well as the data files) was to explicitly set EMBOSS_ACDROOT and EMBOSS_DATA.  Oddly, installing libx11-devel and removing the '--without-x' flag during configuration worked just fine, no need for default env variables or .embossrc files.

Anyone else run into this?

chris


Christopher Fields
Senior Research Scientist
National Center for Supercomputing Applications
Institute for Genomic Biology
University of Illinois Urbana-Champaign
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801




From cjfields at illinois.edu  Wed Dec  7 02:20:55 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 7 Dec 2011 02:20:55 +0000
Subject: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
In-Reply-To: <5ACBA19439E77B43A06F4CAB897EC97702FA78386C@EXCH1-COLO.accelrys.net>
References: <5ACBA19439E77B43A06F4CAB897EC97702FA783787@EXCH1-COLO.accelrys.net>
	<BD5A1F3D-0EE3-4B8E-9E54-947CCD8D2CCE@illinois.edu>
	<5ACBA19439E77B43A06F4CAB897EC97702FA78386C@EXCH1-COLO.accelrys.net>
Message-ID: <7A5DAABA-33BE-4D94-8224-2353D3C2B90F@illinois.edu>

Yeah, caught Peter's response on that.  Just wanted to make sure there isn't anything we need to do from our end :)

chris
 
On Dec 6, 2011, at 2:21 PM, Scott Markel wrote:

> Chris,
> 
> I don't think so.  We certainly made changes to our BioPerl copy to work around the EMBOSS bug, but I don't think BioPerl needs to incorporate what we did (writing a little subroutine to fix the tags).  An EMBOSS fix takes care of our problem.
> 
> Scott
> 
> 
> -----Original Message-----
> From: Fields, Christopher J [mailto:cjfields at illinois.edu] 
> Sent: Monday, 05 December 05 2011 6:04 PM
> To: Scott Markel
> Cc: emboss at lists.open-bio.org; Kristine Briedis
> Subject: Re: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro
> 
> Scott, is this something that needs to be addressed on the bioperl end?
> 
> chris
> 
> On Dec 5, 2011, at 7:14 PM, Scott Markel wrote:
> 
>> We use BioPerl to build EMBOSS command lines in Pipeline Pilot.  After updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem.  There are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips.  In investigating a bit, it looks like there was a change in the acdtable output.
>> 
>> Here are EMBOSS command lines for embossversion and acdtable.
>> 
>>> embossversion
>> Reports the current EMBOSS version number
>> 6.4.0.2
>> 
>>> acdtable fuzzpro -help -verbose >& fuzzpro_6.4.0.html
>> 
>> And here are the three sets of tag mismatches in the HTML.  All involve an opening <th> and a closing </td>.
>> 
>> Lines 66-9:
>> 
>> <tr bgcolor="#FFFFCC">
>> <th align="left" colspan=5>"-sequence" associated seqall qualifiers </td> </tr>
>> 
>> Lines 183-6:
>> 
>> <tr bgcolor="#FFFFCC">
>> <th align="left" colspan=5>"-pattern" associated pattern qualifiers </td> </tr>
>> 
>> Lines 212-5:
>> 
>> <tr bgcolor="#FFFFCC">
>> <th align="left" colspan=5>"-outfile" associated report qualifiers </td> </tr>
>> 
>> Scott
>> 
>> Scott Markel, Ph.D.
>> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
>> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
>> San Diego, CA 92121                 fax:    +1 858 799 5222
>> USA                                 web:    http://www.accelrys.com
>> 
>> http://www.linkedin.com/in/smarkel
>> Secretary, Board of Directors:
>>    International Society for Computational Biology
>> Chair: ISCB Publications Committee
>> Associate Editor: PLoS Computational Biology
>> Editorial Board: Briefings in Bioinformatics
>> 
>> 
>> 
>> 
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
> 
> 
>