From jrvalverde at cnb.uam.es  Thu Mar  1 03:58:58 2001
From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es)
Date: Thu, 1 Mar 2001 09:58:58 +0100 (MET)
Subject: cirdna, restrict
In-Reply-To: <FC9B7D630C18D411A6C800508BCFDEC127EE2B@edunivexch02.umassmed.edu>
Message-ID: <200103010858.f218wwQ6304036@embnet.cnb.uam.es>

"Lapointe, David" <David.Lapointe at umassmed.edu> wrote:
> For what it is worth, I have had problems converting EMBOSS ps output to PDF
> ( with Adobe Distiller). Prettyplot, for example, produces a great color
> postscript file, but when it is converted to PDF it is all messed up ( Fonts
> WAY TOO LARGE). I was intending to convert the ps output to PDF in the
> background for web viewing and easier printing.  
> 
> I guess I'd like to see an option for PDF output in the list of graphical
> formats.

Have you tried conversion with GhostScript? Perhaps it will work 
better. And it's handier for automatic conversion scripting.

				j





From gbottu at ben.vub.ac.be  Tue Mar  6 07:57:27 2001
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Tue, 6 Mar 2001 13:57:27 +0100 (MET)
Subject: question about mse
Message-ID: <200103061257.NAA23873@bigben.vub.ac.be>

from : BEN

	Dear colleagues,
	
I just tried the mse distributed with EMBOSS (EMBOSS 1.10.0 and MSE 0.0.4 under 
Solaris 2.7). According to the documentation the <backspace> key should make a 
sequence move to the left, on vt200 you should be able to use <ctrl-h> or F12. I 
tried all three in a CDE Terminal, in an Xterm and with TeraTerm, but nothing 
happens.
More seriously, it is not possible to save the modified alignment. When I type 
the command "exit" or "exit xxx", the program asks "Sequences modified do you 
wish to continue exiting [N]" and when I answer "y" the program exits but does 
not produce any output file. Am I missing somethng ?

	Guy Bottu





From gwilliam at hgmp.mrc.ac.uk  Tue Mar  6 08:17:17 2001
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Tue, 06 Mar 2001 13:17:17 +0000
Subject: question about mse
References: <200103061257.NAA23873@bigben.vub.ac.be>
Message-ID: <3AA4E35D.395B124B@hgmp.mrc.ac.uk>

Guy Bottu wrote:

> More seriously, it is not possible to save the modified alignment. When I type
> the command "exit" or "exit xxx", the program asks "Sequences modified do you
> wish to continue exiting [N]" and when I answer "y" the program exits but does
> not produce any output file. Am I missing somethng ?
> 
>         Guy Bottu


The FAQ says:

Q) In the editor 'mse', but I don't know how to save my edited sequences
   at the end of the editing session.

A) Use Control-Z to get into command mode.
   Then use the SAVE command which will prompt for the file name.


-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK





From mlahtela at csc.fi  Tue Mar  6 12:49:13 2001
From: mlahtela at csc.fi (Maija Lahtela)
Date: Tue, 6 Mar 2001 19:49:13 +0200 (EET)
Subject: Etandem in EMBOSS packages
Message-ID: <Pine.LNX.4.10.10103061941031.16034-100000@sampo.csc.fi>

Dear All,

I would like to know how the score ( i.e 120) is calculated in output file
of etandem
120        793        936  6  24  93.8 acccta
 90        283        420  6  23  84.8 taaccc

The other thing that worries me is how to select threshold value. What is
difference if I choose threshold=6 or threshold=10 ?  

Best Regards,
Maija Lahtela-Kakkonen

*****************************************************
Maija Lahtela-Kakkonen, 
Application Scientist / Chemistry
CSC-Scientific Computing
Tekniikantie 15 a D, P.O.Box 405 
FIN-02101 ESPOO  FINLAND
TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302
E-MAIL mlahtela at csc.fi, Internet:www.csc.fi
****************************************************





From peter.rice at uk.lionbioscience.com  Tue Mar  6 13:10:18 2001
From: peter.rice at uk.lionbioscience.com (Peter Rice)
Date: Tue, 06 Mar 2001 18:10:18 +0000
Subject: Etandem in EMBOSS packages
References: <Pine.LNX.4.10.10103061941031.16034-100000@sampo.csc.fi>
Message-ID: <3AA5280A.E549C934@uk.lionbioscience.com>

Maija Lahtela wrote:

> I would like to know how the score ( i.e 120) is calculated in output file
> of etandem
> 120        793        936  6  24  93.8 acccta
>  90        283        420  6  23  84.8 taaccc
> 
> The other thing that worries me is how to select threshold value. What is
> difference if I choose threshold=6 or threshold=10 ?

The algorithm is buried inside Richard Durbin's original version of the
code, and was never documented by the author.

As far as I could tell, from inspecting the code (and this could turn into
part of the program documentation :-) :

sequences are converted into ACGT or N (so ambiguity codes are ignored)
The score is +1 for a match, -1 for a mismatch.
The first copy of a repeat is ignored.
The highest score is kept for each start position and repeat size.

The threshold score is the lowest score to be reported. For perfect
repeats, it is the length of the repeat (except for the first copy). Reduce
it a little to allow mismatches. Each mismatch scores -1 instead of +1 so
it scores 2 less than perfect match in the same number of bases.

Running with a wide range of repeat sizes is inefficient. That is why
equicktandem was written - to give a rapid estimate of the major repeat
sizes.

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723





From s.roehrig at xantos-bio.de  Wed Mar  7 07:54:20 2001
From: s.roehrig at xantos-bio.de (Roehrig, Sascha)
Date: Wed, 7 Mar 2001 13:54:20 +0100 
Subject: abiview
Message-ID: <A31E2A68EB0ED411950A00D0B72601C10EE608@XAN-BDC>

Dear all,
 
I have been trying to get abiview to run. Unfortunately, the program exits
each time with the following error no matter what options I choose. All
other EMBOSS applications are running fine.
 
 
start quote-------->
 
Uncaught exception
 Assertion failed
 raised at ajmem.c:78
 
 
   EMBOSS An error in ajexcept.c at line 56:
aborting.....
 
<----------end quote
 
The tracer files are easily viewed and opened with "Chromas".
 
Any suggestions?
 
Cheers
 
Sascha
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From s.roehrig at xantos-bio.de  Wed Mar  7 07:56:13 2001
From: s.roehrig at xantos-bio.de (Roehrig, Sascha)
Date: Wed, 7 Mar 2001 13:56:13 +0100 
Subject: abiview
Message-ID: <A31E2A68EB0ED411950A00D0B72601C10EE609@XAN-BDC>

Dear all,
 
I have been trying to get abiview to run. Unfortunately, the program exits
each time with the following error no matter what options I choose. All
other EMBOSS applications are running fine.
 
 
start quote-------->
 
Uncaught exception
 Assertion failed
 raised at ajmem.c:78
 
 
   EMBOSS An error in ajexcept.c at line 56:
aborting.....
 
<----------end quote
 
The tracer files are easily viewed and opened with "Chromas".
 
Any suggestions?
 
Cheers
 
Sascha

<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />


 
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From s.roehrig at xantos-bio.de  Wed Mar  7 10:02:31 2001
From: s.roehrig at xantos-bio.de (Roehrig, Sascha)
Date: Wed, 7 Mar 2001 16:02:31 +0100 
Subject: abiview
Message-ID: <A31E2A68EB0ED411950A00D0B72601C10EE60A@XAN-BDC>

Dear Tim,
 
I am running Emboss locally under Redhat 6.2.
Abiview produces the same error whether told to produce x11 or postscript
output. Starting the application under xwindows didn't help either.
I have not been able to run abiview with any ABI files, however, since
Chromas was able to open them I concluded that the integrity of the files is
ok. However, the tracer files all stem from the same sequencing company, so
maybe there is some problem there. 
 
Maybe you can send me one abi file, which works for you, so I can test it
locally here.
 
Best regards,
 
Sascha

-----Original Message-----
From: Tim Carver [mailto:tcarver at hgmp.mrc.ac.uk]
Sent: Wednesday, March 07, 2001 2:47 PM
To: Roehrig, Sascha
Subject: Re: abiview


Dear Sascha, 

   Sorry to hear about the problem you are having running abiview. It is
difficult to tell from the error message that you get as to what the problem
may actually be.  Have you been able to successfully run abiview with any
ABI files? What operating system are you using ? (I guess you are using your
own local version of Emboss). I'm not familiar with Chromas but I notice
it's a windows application. Have you got XWindows enabled on your machine
(i.e. are you using software like eXceed if you are using a pc). 


   Apologies to answer your question with more questions but it would help
in understanding the nature of the problem. 


Best Regards 
Tim Carver 
  


", Sascha" wrote: 


Dear all,I have been trying to get abiview to run. Unfortunately, the
program exits each time with the following error no matter what options I
choose. All other EMBOSS applications are running fine.start
quote-------->Uncaught exception Assertion failed raised at ajmem.c:78
EMBOSS An error in ajexcept.c at line 56:aborting.....<----------end
quoteThe tracer files are easily viewed and opened with "Chromas".Any
suggestions?CheersSascha 
<?xml:namespace prefix = o ns = " urn:schemas-microsoft-com:office:office
<urn:schemas-microsoft-com:office:office> " />

-- 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Tim Carver, PhD,      

Bioinformatics, MRC HGMP Resource Centre,

Hinxton, Cambridge, CB10 1SB

Tel: +44 1223 494 532 Fax: +44 1223 494512

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  

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From sgmd at genetik.fu-berlin.de  Mon Mar 12 05:18:20 2001
From: sgmd at genetik.fu-berlin.de (Thomas Siegmund)
Date: Mon, 12 Mar 2001 11:18:20 +0100
Subject: Announce: A GUI for EMBOSS applications
Message-ID: <01031211182002.25152@scarlet>

Hello everybody,

on this list I do not have to praise the EMBOSS package for its quality and 
its wealth of functions. In my opinion EMBOSS on a standard PC running Linux 
makes a fairly complete system for everyday use in a molecular biology 
laboratory. There is only one problem: Up to now, EMBOSS lacks a graphical 
user interface which allows the occasional user to access its functionality 
in an easy way. Therefore, I have started to wrap a simple GUI around some of 
the most often used EMBOSS applications (*).

My favorite desktop is KDE, a graphical environment which runs on almost any 
variety of Unix, of course also on Linux. KDE is the default desktop on SuSE 
and Mandrake Linux. On top of this I used "Kaptain" for building KDE GUIs for 
EMBOSS applications. Kaptain is a universally applicable graphical front-end 
based on context-free grammars. It is a KDE2 application, but you can run it 
also from Gnome if at least the QT libraries are installed. All of this is 
open source software.

For the first few MBOSS applications (*) I have written such grammars, 
which can be started directly from the desktop or from a shell. The 
grammars are interpreted by Kaptain, which in turn presents a nice dialog box 
with all options and parameters for a specific EMBOSS application. The user 
makes all necessary adjustments via mouse and keyboard and then runs the 
EMBOSS application from the dialog. A preview button allows to play with the 
settings until the best combination is found. Files can be selected with 
the standard KDE file select box. The large number of options in the more 
complex EMBOSS applications are presented in a structured way. Additional 
tooltips for many checkboxes and buttons provide informations about the 
parameters (as much as I can tell from the EMBOSS documentation).

I know, that there are some other GUI projects for EMBOSS and I don't want to 
compete with them. As far as I understand, these projects are client-server 
approaches what probably makes them well suited for larger institutions. My 
simple GUI wrapper based on Kaptain on the other hand runs without 
complicated setup on any recent standalone linux box (and probably on 
anything else which has an X server). The nice thing about Kaptain grammars 
is its simlicity. You can very quickly write a grammar for any command line 
application. The grammars I have finished so far only take 100 - 200 lines of 
code, half of it often used for tooltips. Most of the time I spent reading 
teh EMBOSS documentation. Of course such a simple solution has limitations. 
The most important differences to a GUI written in a programming language (as 
opposed to a grammar) are (1) limited input checking and (2) the missing 
"save user defaults" function. Therefore, I am pretty sure that better GUIs 
for EMBOSS will come after the Kaptain grammars. 

If you would like to give the Kaptain grammars for EMBOSS a try, please visit 
my web site at http://userpage.fu-berlin.de/~sgmd/ . There you will find some 
more details, a few screenshots and of course a download page. Any feedback 
is highly appreciated.

Many thanks to all the EMBOSS developers for providing a great open source 
package for sequence analyis.

With best regards

Thomas Siegmund

(*) 
backtranseq, remap, dotmatcher, restrict, est2genome, revseq, getorf, seqret,
needle, water, showseq, plotorf, syco

-- 
Free University of Berlin
Institut of Genetics
Arnimallee 7
14195 Berlin
Germany
Tel: +49 30 838 54868





From oddmund.nordgard at biokjemi.uio.no  Mon Mar 12 05:39:31 2001
From: oddmund.nordgard at biokjemi.uio.no (=?ISO-8859-1?Q?Oddmund_Nordg=E5rd?=)
Date: Mon, 12 Mar 2001 11:39:31 +0100 (CET)
Subject: Announce: A GUI for EMBOSS applications
In-Reply-To: <01031211182002.25152@scarlet>
Message-ID: <Pine.LNX.4.30.0103121138270.10077-100000@david.uio.no>


Great idea to use Kaptain with EMBOSS!
I`ll try it.

Oddmund

-- 
*******************************************

  Oddmund Nordg?rd
  Ph.D. student
  Institute of Biochemistry
  Box 1041 Blindern
  0316 OSLO
  NORWAY
  Phone: 22 85 66 99
  Fax:   22 85 44 43
  Email: oddmundn at biokjemi.uio.no

  Private:
  Kalbakkv. 21
  0953 OSLO
  Phone: 22 25 23 93

********************************************
Powered by Linux! http://www.linuxnorge.com







From jweiner1 at ix.urz.uni-heidelberg.de  Thu Mar 22 07:03:15 2001
From: jweiner1 at ix.urz.uni-heidelberg.de (January Weiner 3)
Date: Thu, 22 Mar 2001 13:03:15 +0100 (CET)
Subject: GUI for EMBOS
In-Reply-To: <200102261648.QAA20498@tin.hgmp.mrc.ac.uk>
Message-ID: <Pine.A41.4.20.0103221253420.53110-100000@aixterm1.urz.uni-heidelberg.de>

Hello,
	I have created a small program called 'Arka'. It was thought as a
	GUI frontend for a small pack of EMBOSS-like tools I have created
	on my own, but it can serve as well as a GUI for any command-line
	programs. 

	Arka reads a text file with the descriptions of the program you'd
	like to use, and makes a menu entry for the program. Then, if you
	select the menu, it gives you a dialog with all the options you
	have put in the description file. The format of the description
	file is right now a little messy, you can take a look at the
	description file for my command line programs, but basically it is
	quite extendable and flexible. The next version of arka will have a
	gui for creating the spec files. Right now it is something between
	an alpha and a beta version, and I'd like to know whether anybody
	is interested in it at all.

	Arka is nothing very complicated, but as with all my programs, I
	wanted it to be fast and resource-friendly, and independent of
	GNOME or any other bloated environments. It is written in C with
	Gtk+ and runs quickly on a 486. It is something in between a real
	GUI and command line. A smart `crouch' that remembers the options,
	that's all.

	More information + download (source / rpms): 
	http://www.bioinformatics.org/genpak/

	BTW arka is GPLed, of course.

	Best regards,
	January


----)-\//-///-----------------------------------January-Weiner-3-------
Did you hear about the biologist who had twins? 
She baptized one and kept the other as a control.



From kumar at ipk-gatersleben.de  Tue Mar 27 02:03:31 2001
From: kumar at ipk-gatersleben.de (Dr. Rajeev Kumar)
Date: Tue, 27 Mar 2001 09:03:31 +0200
Subject: Joining the mailing list
Message-ID: <3AC03B43.992A2A65@ipk-gatersleben.de>

Please include my name on your list.

Thanks,

Rajeev
-- 
************************************************************
Rajeev Kumar (Varshney), Ph.D.
Molecular Markers Group, Genomzentrum
Institut f?r Pflanzengenetik und Kulturpflanzenforschung 
IPK, Corrensstra?e 3
D 06466 GATERSLEBEN,
GERMANY 
Tel(off):++ 49 (0)39482 5594
   (lab):++ 49 (0)39482 5231 
Fax     :++ 49 (0)39482 5595 
e-mail  :rajeev at ipk-gatersleben.de
         rajeevkvarshney at hotmail.com
web page:http://www.ipk-gatersleben.de 
************************************************************



From gbottu at ben.vub.ac.be  Wed Mar 28 05:58:12 2001
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Wed, 28 Mar 2001 12:58:12 +0200 (MET DST)
Subject: are we losing TRANSFAC ?
Message-ID: <200103281058.MAA22612@bigben.vub.ac.be>

from : BEN

	Dear colleagues,
	
One of the facilities of EMBOSS is access to the TRANSFAC databank through the 
tfscan program. This program risks however to become obsolete, at least for the 
EMBnet Nodes. The TRANSFAC databank from release 5 on has become commercial. You 
must pay to have downloadable flat files and you are not allowed to give access 
to third parties (see http://www.gene-regulation.com). 
Is anyone aware of a solution ? Maybe a special arrangement for EMBnet ? Or 
should we use instead the TFD databank (http://www.ifto.org) ? But that one is 
less complete and the last version dates from April 2000.

 	Guy Bottu



From P.Ernst at DKFZ-Heidelberg.de  Wed Mar 28 11:06:00 2001
From: P.Ernst at DKFZ-Heidelberg.de (Peter Ernst)
Date: Wed, 28 Mar 2001 18:06:00 +0200 (MET DST)
Subject: Announcement: W2H version 4.0 released (EMBOSS-GUI)
Message-ID: <Pine.GSO.4.21.0103281758450.663-100000@husar.inet.dkfz-heidelberg.de>

Dear EMBOSSians,

I am pleased to announce a new release (4.0)
of "W2H - the WWW Interface to Sequence Analysis Software Tools".
 
This is the first release with support for EMBOSS, however the support
for the GCG package continues.
 
For further details, please check the W2H homepage.
 
Availability:
 
   ftp://genome.dkfz-heidelberg.de/pub/w2h    and/or
   ftp://ftp.ebi.ac.uk/pub/software/unix/w2h
 
W2H homepage:
 
   http://www.w2h.dkfz-heidelberg.de/   and/or
   http://industry.ebi.ac.uk/w2h
 
Peter Ernst



From bauer at genprofile.com  Thu Mar 29 05:03:07 2001
From: bauer at genprofile.com (David Bauer)
Date: Thu, 29 Mar 2001 12:03:07 +0200
Subject: est2genome
Message-ID: <3AC3085B.D0AD99BB@genprofile.com>

Hi,

just an info for est2genome users.

I found est2genome having problems finding very short exons with the
default parameters.

With the folowing changes it detects also a 14bp exon correctly:

mismatch 1 -> 3
intronpenalty 40 -> 20
splicepenalty 20 -> 10
minscore 30 -> 10

David
-- 
Dr. David Bauer
GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus 
Robert-Roessle-Str. 10, D-13125 Berlin, Germany
bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151




From jrvalverde at cnb.uam.es  Thu Mar  1 08:58:58 2001
From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es)
Date: Thu, 1 Mar 2001 09:58:58 +0100 (MET)
Subject: cirdna, restrict
In-Reply-To: <FC9B7D630C18D411A6C800508BCFDEC127EE2B@edunivexch02.umassmed.edu>
Message-ID: <200103010858.f218wwQ6304036@embnet.cnb.uam.es>

"Lapointe, David" <David.Lapointe at umassmed.edu> wrote:
> For what it is worth, I have had problems converting EMBOSS ps output to PDF
> ( with Adobe Distiller). Prettyplot, for example, produces a great color
> postscript file, but when it is converted to PDF it is all messed up ( Fonts
> WAY TOO LARGE). I was intending to convert the ps output to PDF in the
> background for web viewing and easier printing.  
> 
> I guess I'd like to see an option for PDF output in the list of graphical
> formats.

Have you tried conversion with GhostScript? Perhaps it will work 
better. And it's handier for automatic conversion scripting.

				j





From gbottu at ben.vub.ac.be  Tue Mar  6 12:57:27 2001
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Tue, 6 Mar 2001 13:57:27 +0100 (MET)
Subject: question about mse
Message-ID: <200103061257.NAA23873@bigben.vub.ac.be>

from : BEN

	Dear colleagues,
	
I just tried the mse distributed with EMBOSS (EMBOSS 1.10.0 and MSE 0.0.4 under 
Solaris 2.7). According to the documentation the <backspace> key should make a 
sequence move to the left, on vt200 you should be able to use <ctrl-h> or F12. I 
tried all three in a CDE Terminal, in an Xterm and with TeraTerm, but nothing 
happens.
More seriously, it is not possible to save the modified alignment. When I type 
the command "exit" or "exit xxx", the program asks "Sequences modified do you 
wish to continue exiting [N]" and when I answer "y" the program exits but does 
not produce any output file. Am I missing somethng ?

	Guy Bottu





From gwilliam at hgmp.mrc.ac.uk  Tue Mar  6 13:17:17 2001
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Tue, 06 Mar 2001 13:17:17 +0000
Subject: question about mse
References: <200103061257.NAA23873@bigben.vub.ac.be>
Message-ID: <3AA4E35D.395B124B@hgmp.mrc.ac.uk>

Guy Bottu wrote:

> More seriously, it is not possible to save the modified alignment. When I type
> the command "exit" or "exit xxx", the program asks "Sequences modified do you
> wish to continue exiting [N]" and when I answer "y" the program exits but does
> not produce any output file. Am I missing somethng ?
> 
>         Guy Bottu


The FAQ says:

Q) In the editor 'mse', but I don't know how to save my edited sequences
   at the end of the editing session.

A) Use Control-Z to get into command mode.
   Then use the SAVE command which will prompt for the file name.


-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK





From mlahtela at csc.fi  Tue Mar  6 17:49:13 2001
From: mlahtela at csc.fi (Maija Lahtela)
Date: Tue, 6 Mar 2001 19:49:13 +0200 (EET)
Subject: Etandem in EMBOSS packages
Message-ID: <Pine.LNX.4.10.10103061941031.16034-100000@sampo.csc.fi>

Dear All,

I would like to know how the score ( i.e 120) is calculated in output file
of etandem
120        793        936  6  24  93.8 acccta
 90        283        420  6  23  84.8 taaccc

The other thing that worries me is how to select threshold value. What is
difference if I choose threshold=6 or threshold=10 ?  

Best Regards,
Maija Lahtela-Kakkonen

*****************************************************
Maija Lahtela-Kakkonen, 
Application Scientist / Chemistry
CSC-Scientific Computing
Tekniikantie 15 a D, P.O.Box 405 
FIN-02101 ESPOO  FINLAND
TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302
E-MAIL mlahtela at csc.fi, Internet:www.csc.fi
****************************************************





From peter.rice at uk.lionbioscience.com  Tue Mar  6 18:10:18 2001
From: peter.rice at uk.lionbioscience.com (Peter Rice)
Date: Tue, 06 Mar 2001 18:10:18 +0000
Subject: Etandem in EMBOSS packages
References: <Pine.LNX.4.10.10103061941031.16034-100000@sampo.csc.fi>
Message-ID: <3AA5280A.E549C934@uk.lionbioscience.com>

Maija Lahtela wrote:

> I would like to know how the score ( i.e 120) is calculated in output file
> of etandem
> 120        793        936  6  24  93.8 acccta
>  90        283        420  6  23  84.8 taaccc
> 
> The other thing that worries me is how to select threshold value. What is
> difference if I choose threshold=6 or threshold=10 ?

The algorithm is buried inside Richard Durbin's original version of the
code, and was never documented by the author.

As far as I could tell, from inspecting the code (and this could turn into
part of the program documentation :-) :

sequences are converted into ACGT or N (so ambiguity codes are ignored)
The score is +1 for a match, -1 for a mismatch.
The first copy of a repeat is ignored.
The highest score is kept for each start position and repeat size.

The threshold score is the lowest score to be reported. For perfect
repeats, it is the length of the repeat (except for the first copy). Reduce
it a little to allow mismatches. Each mismatch scores -1 instead of +1 so
it scores 2 less than perfect match in the same number of bases.

Running with a wide range of repeat sizes is inefficient. That is why
equicktandem was written - to give a rapid estimate of the major repeat
sizes.

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723





From s.roehrig at xantos-bio.de  Wed Mar  7 12:54:20 2001
From: s.roehrig at xantos-bio.de (Roehrig, Sascha)
Date: Wed, 7 Mar 2001 13:54:20 +0100 
Subject: abiview
Message-ID: <A31E2A68EB0ED411950A00D0B72601C10EE608@XAN-BDC>

Dear all,
 
I have been trying to get abiview to run. Unfortunately, the program exits
each time with the following error no matter what options I choose. All
other EMBOSS applications are running fine.
 
 
start quote-------->
 
Uncaught exception
 Assertion failed
 raised at ajmem.c:78
 
 
   EMBOSS An error in ajexcept.c at line 56:
aborting.....
 
<----------end quote
 
The tracer files are easily viewed and opened with "Chromas".
 
Any suggestions?
 
Cheers
 
Sascha
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From s.roehrig at xantos-bio.de  Wed Mar  7 12:56:13 2001
From: s.roehrig at xantos-bio.de (Roehrig, Sascha)
Date: Wed, 7 Mar 2001 13:56:13 +0100 
Subject: abiview
Message-ID: <A31E2A68EB0ED411950A00D0B72601C10EE609@XAN-BDC>

Dear all,
 
I have been trying to get abiview to run. Unfortunately, the program exits
each time with the following error no matter what options I choose. All
other EMBOSS applications are running fine.
 
 
start quote-------->
 
Uncaught exception
 Assertion failed
 raised at ajmem.c:78
 
 
   EMBOSS An error in ajexcept.c at line 56:
aborting.....
 
<----------end quote
 
The tracer files are easily viewed and opened with "Chromas".
 
Any suggestions?
 
Cheers
 
Sascha

<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />


 
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From s.roehrig at xantos-bio.de  Wed Mar  7 15:02:31 2001
From: s.roehrig at xantos-bio.de (Roehrig, Sascha)
Date: Wed, 7 Mar 2001 16:02:31 +0100 
Subject: abiview
Message-ID: <A31E2A68EB0ED411950A00D0B72601C10EE60A@XAN-BDC>

Dear Tim,
 
I am running Emboss locally under Redhat 6.2.
Abiview produces the same error whether told to produce x11 or postscript
output. Starting the application under xwindows didn't help either.
I have not been able to run abiview with any ABI files, however, since
Chromas was able to open them I concluded that the integrity of the files is
ok. However, the tracer files all stem from the same sequencing company, so
maybe there is some problem there. 
 
Maybe you can send me one abi file, which works for you, so I can test it
locally here.
 
Best regards,
 
Sascha

-----Original Message-----
From: Tim Carver [mailto:tcarver at hgmp.mrc.ac.uk]
Sent: Wednesday, March 07, 2001 2:47 PM
To: Roehrig, Sascha
Subject: Re: abiview


Dear Sascha, 

   Sorry to hear about the problem you are having running abiview. It is
difficult to tell from the error message that you get as to what the problem
may actually be.  Have you been able to successfully run abiview with any
ABI files? What operating system are you using ? (I guess you are using your
own local version of Emboss). I'm not familiar with Chromas but I notice
it's a windows application. Have you got XWindows enabled on your machine
(i.e. are you using software like eXceed if you are using a pc). 


   Apologies to answer your question with more questions but it would help
in understanding the nature of the problem. 


Best Regards 
Tim Carver 
  


", Sascha" wrote: 


Dear all,I have been trying to get abiview to run. Unfortunately, the
program exits each time with the following error no matter what options I
choose. All other EMBOSS applications are running fine.start
quote-------->Uncaught exception Assertion failed raised at ajmem.c:78
EMBOSS An error in ajexcept.c at line 56:aborting.....<----------end
quoteThe tracer files are easily viewed and opened with "Chromas".Any
suggestions?CheersSascha 
<?xml:namespace prefix = o ns = " urn:schemas-microsoft-com:office:office
<urn:schemas-microsoft-com:office:office> " />

-- 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Tim Carver, PhD,      

Bioinformatics, MRC HGMP Resource Centre,

Hinxton, Cambridge, CB10 1SB

Tel: +44 1223 494 532 Fax: +44 1223 494512

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  

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From sgmd at genetik.fu-berlin.de  Mon Mar 12 10:18:20 2001
From: sgmd at genetik.fu-berlin.de (Thomas Siegmund)
Date: Mon, 12 Mar 2001 11:18:20 +0100
Subject: Announce: A GUI for EMBOSS applications
Message-ID: <01031211182002.25152@scarlet>

Hello everybody,

on this list I do not have to praise the EMBOSS package for its quality and 
its wealth of functions. In my opinion EMBOSS on a standard PC running Linux 
makes a fairly complete system for everyday use in a molecular biology 
laboratory. There is only one problem: Up to now, EMBOSS lacks a graphical 
user interface which allows the occasional user to access its functionality 
in an easy way. Therefore, I have started to wrap a simple GUI around some of 
the most often used EMBOSS applications (*).

My favorite desktop is KDE, a graphical environment which runs on almost any 
variety of Unix, of course also on Linux. KDE is the default desktop on SuSE 
and Mandrake Linux. On top of this I used "Kaptain" for building KDE GUIs for 
EMBOSS applications. Kaptain is a universally applicable graphical front-end 
based on context-free grammars. It is a KDE2 application, but you can run it 
also from Gnome if at least the QT libraries are installed. All of this is 
open source software.

For the first few MBOSS applications (*) I have written such grammars, 
which can be started directly from the desktop or from a shell. The 
grammars are interpreted by Kaptain, which in turn presents a nice dialog box 
with all options and parameters for a specific EMBOSS application. The user 
makes all necessary adjustments via mouse and keyboard and then runs the 
EMBOSS application from the dialog. A preview button allows to play with the 
settings until the best combination is found. Files can be selected with 
the standard KDE file select box. The large number of options in the more 
complex EMBOSS applications are presented in a structured way. Additional 
tooltips for many checkboxes and buttons provide informations about the 
parameters (as much as I can tell from the EMBOSS documentation).

I know, that there are some other GUI projects for EMBOSS and I don't want to 
compete with them. As far as I understand, these projects are client-server 
approaches what probably makes them well suited for larger institutions. My 
simple GUI wrapper based on Kaptain on the other hand runs without 
complicated setup on any recent standalone linux box (and probably on 
anything else which has an X server). The nice thing about Kaptain grammars 
is its simlicity. You can very quickly write a grammar for any command line 
application. The grammars I have finished so far only take 100 - 200 lines of 
code, half of it often used for tooltips. Most of the time I spent reading 
teh EMBOSS documentation. Of course such a simple solution has limitations. 
The most important differences to a GUI written in a programming language (as 
opposed to a grammar) are (1) limited input checking and (2) the missing 
"save user defaults" function. Therefore, I am pretty sure that better GUIs 
for EMBOSS will come after the Kaptain grammars. 

If you would like to give the Kaptain grammars for EMBOSS a try, please visit 
my web site at http://userpage.fu-berlin.de/~sgmd/ . There you will find some 
more details, a few screenshots and of course a download page. Any feedback 
is highly appreciated.

Many thanks to all the EMBOSS developers for providing a great open source 
package for sequence analyis.

With best regards

Thomas Siegmund

(*) 
backtranseq, remap, dotmatcher, restrict, est2genome, revseq, getorf, seqret,
needle, water, showseq, plotorf, syco

-- 
Free University of Berlin
Institut of Genetics
Arnimallee 7
14195 Berlin
Germany
Tel: +49 30 838 54868





From oddmund.nordgard at biokjemi.uio.no  Mon Mar 12 10:39:31 2001
From: oddmund.nordgard at biokjemi.uio.no (=?ISO-8859-1?Q?Oddmund_Nordg=E5rd?=)
Date: Mon, 12 Mar 2001 11:39:31 +0100 (CET)
Subject: Announce: A GUI for EMBOSS applications
In-Reply-To: <01031211182002.25152@scarlet>
Message-ID: <Pine.LNX.4.30.0103121138270.10077-100000@david.uio.no>


Great idea to use Kaptain with EMBOSS!
I`ll try it.

Oddmund

-- 
*******************************************

  Oddmund Nordg?rd
  Ph.D. student
  Institute of Biochemistry
  Box 1041 Blindern
  0316 OSLO
  NORWAY
  Phone: 22 85 66 99
  Fax:   22 85 44 43
  Email: oddmundn at biokjemi.uio.no

  Private:
  Kalbakkv. 21
  0953 OSLO
  Phone: 22 25 23 93

********************************************
Powered by Linux! http://www.linuxnorge.com







From jweiner1 at ix.urz.uni-heidelberg.de  Thu Mar 22 12:03:15 2001
From: jweiner1 at ix.urz.uni-heidelberg.de (January Weiner 3)
Date: Thu, 22 Mar 2001 13:03:15 +0100 (CET)
Subject: GUI for EMBOS
In-Reply-To: <200102261648.QAA20498@tin.hgmp.mrc.ac.uk>
Message-ID: <Pine.A41.4.20.0103221253420.53110-100000@aixterm1.urz.uni-heidelberg.de>

Hello,
	I have created a small program called 'Arka'. It was thought as a
	GUI frontend for a small pack of EMBOSS-like tools I have created
	on my own, but it can serve as well as a GUI for any command-line
	programs. 

	Arka reads a text file with the descriptions of the program you'd
	like to use, and makes a menu entry for the program. Then, if you
	select the menu, it gives you a dialog with all the options you
	have put in the description file. The format of the description
	file is right now a little messy, you can take a look at the
	description file for my command line programs, but basically it is
	quite extendable and flexible. The next version of arka will have a
	gui for creating the spec files. Right now it is something between
	an alpha and a beta version, and I'd like to know whether anybody
	is interested in it at all.

	Arka is nothing very complicated, but as with all my programs, I
	wanted it to be fast and resource-friendly, and independent of
	GNOME or any other bloated environments. It is written in C with
	Gtk+ and runs quickly on a 486. It is something in between a real
	GUI and command line. A smart `crouch' that remembers the options,
	that's all.

	More information + download (source / rpms): 
	http://www.bioinformatics.org/genpak/

	BTW arka is GPLed, of course.

	Best regards,
	January


----)-\//-///-----------------------------------January-Weiner-3-------
Did you hear about the biologist who had twins? 
She baptized one and kept the other as a control.



From kumar at ipk-gatersleben.de  Tue Mar 27 07:03:31 2001
From: kumar at ipk-gatersleben.de (Dr. Rajeev Kumar)
Date: Tue, 27 Mar 2001 09:03:31 +0200
Subject: Joining the mailing list
Message-ID: <3AC03B43.992A2A65@ipk-gatersleben.de>

Please include my name on your list.

Thanks,

Rajeev
-- 
************************************************************
Rajeev Kumar (Varshney), Ph.D.
Molecular Markers Group, Genomzentrum
Institut f?r Pflanzengenetik und Kulturpflanzenforschung 
IPK, Corrensstra?e 3
D 06466 GATERSLEBEN,
GERMANY 
Tel(off):++ 49 (0)39482 5594
   (lab):++ 49 (0)39482 5231 
Fax     :++ 49 (0)39482 5595 
e-mail  :rajeev at ipk-gatersleben.de
         rajeevkvarshney at hotmail.com
web page:http://www.ipk-gatersleben.de 
************************************************************



From gbottu at ben.vub.ac.be  Wed Mar 28 10:58:12 2001
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Wed, 28 Mar 2001 12:58:12 +0200 (MET DST)
Subject: are we losing TRANSFAC ?
Message-ID: <200103281058.MAA22612@bigben.vub.ac.be>

from : BEN

	Dear colleagues,
	
One of the facilities of EMBOSS is access to the TRANSFAC databank through the 
tfscan program. This program risks however to become obsolete, at least for the 
EMBnet Nodes. The TRANSFAC databank from release 5 on has become commercial. You 
must pay to have downloadable flat files and you are not allowed to give access 
to third parties (see http://www.gene-regulation.com). 
Is anyone aware of a solution ? Maybe a special arrangement for EMBnet ? Or 
should we use instead the TFD databank (http://www.ifto.org) ? But that one is 
less complete and the last version dates from April 2000.

 	Guy Bottu



From P.Ernst at DKFZ-Heidelberg.de  Wed Mar 28 16:06:00 2001
From: P.Ernst at DKFZ-Heidelberg.de (Peter Ernst)
Date: Wed, 28 Mar 2001 18:06:00 +0200 (MET DST)
Subject: Announcement: W2H version 4.0 released (EMBOSS-GUI)
Message-ID: <Pine.GSO.4.21.0103281758450.663-100000@husar.inet.dkfz-heidelberg.de>

Dear EMBOSSians,

I am pleased to announce a new release (4.0)
of "W2H - the WWW Interface to Sequence Analysis Software Tools".
 
This is the first release with support for EMBOSS, however the support
for the GCG package continues.
 
For further details, please check the W2H homepage.
 
Availability:
 
   ftp://genome.dkfz-heidelberg.de/pub/w2h    and/or
   ftp://ftp.ebi.ac.uk/pub/software/unix/w2h
 
W2H homepage:
 
   http://www.w2h.dkfz-heidelberg.de/   and/or
   http://industry.ebi.ac.uk/w2h
 
Peter Ernst



From bauer at genprofile.com  Thu Mar 29 10:03:07 2001
From: bauer at genprofile.com (David Bauer)
Date: Thu, 29 Mar 2001 12:03:07 +0200
Subject: est2genome
Message-ID: <3AC3085B.D0AD99BB@genprofile.com>

Hi,

just an info for est2genome users.

I found est2genome having problems finding very short exons with the
default parameters.

With the folowing changes it detects also a 14bp exon correctly:

mismatch 1 -> 3
intronpenalty 40 -> 20
splicepenalty 20 -> 10
minscore 30 -> 10

David
-- 
Dr. David Bauer
GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus 
Robert-Roessle-Str. 10, D-13125 Berlin, Germany
bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151