From daniel.rozenbaum at USPTO.GOV  Tue Oct  2 11:02:57 2012
From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc))
Date: Tue, 2 Oct 2012 11:02:57 -0400
Subject: [EMBOSS] fuzzpro memory consumption
Message-ID: <DBE16BB60D08774ABFD9473DD60A73D350D697AE@EMAIL02.uspto.gov>

Dear all,

We attempted to run a fuzzpro search of the UniProt database with the following pattern:

[LIVMSTAC]-[LIVMFYWSTAGC]-[LIMSTAG]-[LIVMSTAGC]-x(2)-[DN]-x-{P}- [LIVMWSTAC]-{DP}-[LIVMFSTAG]-W-[DEN]-[LIVMFSTAGCN]

The job appears to have brought the server into a hung state, and my best guess is that the process consumed so much memory that it caused heavy swapping.

I'm still not 100% sure that my assumption is correct, but in any event, is there a way to gauge how much memory will a fuzznuc/pro or dreg/preg job consume, based on the complexity of the pattern, size of the database, expected number of matches, etc?

Many thanks,
Daniel

--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/Office of Application Engineering & Development/Patent System Division
600 Dulany St.
Alexandria, VA 22314



From daniel.rozenbaum at USPTO.GOV  Fri Oct 12 17:27:56 2012
From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc))
Date: Fri, 12 Oct 2012 17:27:56 -0400
Subject: [EMBOSS] Space in USA "db:seqname" in list file causes unintended
	behavior
Message-ID: <DBE16BB60D08774ABFD9473DD60A73D350D6982F@EMAIL02.uspto.gov>

Hello everyone,

We have encountered the following issue: if there's an erroneous (most likely unintentionally) entry in a list file that looks like "db:<space character>seqname", EMBOSS doesn't issue an error/warning message, but treats this entry as "db:*". Here's an example using the test database tsw in EMBOSS distribution; it contains 100 sequences, three of which match the pattern "hba*" :

% seqret tsw -auto -stdout  | egrep "^>" | wc -l
100
% cat list2
tsw:hba*
% seqret list::list2 -auto -stdout  | egrep "^>" | wc -l
3
% cat list1
tsw: hba*
% seqret list::list1 -auto -stdout  | egrep "^>" | wc -l
100
Of course, the immediate answer is to instruct the users to be careful not to allow unintended spaces in the USA's. Might it be possible though to add some protection against potentially problematic consequences if such an error in the USA is made? In one such instance the resultant clustalw process ended up attempting to build a multiple alignment across the entire UniProt, which the server didn't handle well :-)

With best regards,
Daniel

--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/ Office of Application Engineering & Development/ Patent System Division
600 Dulany St.
Alexandria, VA 22314


From ricepeterm at yahoo.co.uk  Sat Oct 13 03:40:15 2012
From: ricepeterm at yahoo.co.uk (Peter Rice)
Date: Sat, 13 Oct 2012 08:40:15 +0100
Subject: [EMBOSS] Space in USA "db:seqname" in list file causes
 unintended behavior
In-Reply-To: <DBE16BB60D08774ABFD9473DD60A73D350D6982F@EMAIL02.uspto.gov>
References: <DBE16BB60D08774ABFD9473DD60A73D350D6982F@EMAIL02.uspto.gov>
Message-ID: <50791ADF.1040608@yahoo.co.uk>

On 12/10/2012 22:27, Rozenbaum, Daniel (Biocceleration Inc) wrote:
> Hello everyone,
>
> We have encountered the following issue: if there's an erroneous (most likely unintentionally) entry in a list file that looks like "db:<space character>seqname", EMBOSS doesn't issue an error/warning message, but treats this entry as "db:*". >
>
> Might it be possible though to add some protection against potentially problematic consequences if such an error in the USA is made? In one such instance the resultant clustalw process ended up attempting to build a multiple alignment across the entire UniProt, which the server didn't handle well :-)

An interesting problem. List files have a long history, going back 
before EMBOSS. They were also used in the GCG (Wisconsin) package, which 
in turn adopted them from the VMS operating system. where they could be 
used for mailing lists (sending to @list with a list of usernames, for 
example).

In a list file, only the first token (word) is significant. The 
remainder of the line is treated as a comment.

As you discovered, a space before the id (or indeed just a database 
name) is a valid input representing all entries in the database.

I think it is safe to assume that list files in practice have no 
comments, so we can make a simple change for the next release:

list:: indicates a list file with only one token per line. Any 
extraneous text will result in an error or warning message

The same restriction will be applied to the VMS syntax @listfile

A new list style can be added to allow comments so that any user with 
them can still use their list files.

Possibly a stricter comment style could be allowed in standard list:: 
files. We can check what other packages may have introduced, but 
something like a perl-style #comment could be simple to add. The # 
character has no special meaning in the EMBOSS query language.

With those changes in place your users would be saved from extra spaces 
... but of course would still be caught by a newline creeping in to 
start a new record after the database name (reading the entire database, 
then reading the id as a possible filename). Users will get an error 
message from that so long as the second part is not a valid filename or 
database name.

regards,

Peter Rice
EMBOSS Team



From ivaylo.stoimenov at gmail.com  Mon Oct 15 08:03:27 2012
From: ivaylo.stoimenov at gmail.com (Ivaylo Stoimenov)
Date: Mon, 15 Oct 2012 14:03:27 +0200
Subject: [EMBOSS] EMBOSS/Primer3
Message-ID: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>

Hi,

I am wondering if it is possible to pass some of the newest options to
Primer 3, through EMBOSS eprimer32 wrapper. For example, an extremely
useful option will be: "SEQUENCE_PRIMER_PAIR_OK_REGION_LIST=,,2950,50",
which I am not sure how to address, especially in Python. Any suggestion
how to turn this option on or any other additional argument for Primer3
through eprimer32 interface?

Reagrds,
Ivaylo

From ricepeterm at yahoo.co.uk  Mon Oct 15 10:00:33 2012
From: ricepeterm at yahoo.co.uk (Peter Rice)
Date: Mon, 15 Oct 2012 15:00:33 +0100
Subject: [EMBOSS] EMBOSS/Primer3
In-Reply-To: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
References: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
Message-ID: <507C1701.9040403@yahoo.co.uk>

On 15/10/2012 13:03, Ivaylo Stoimenov wrote:
> Hi,
>
> I am wondering if it is possible to pass some of the newest options to
> Primer 3, through EMBOSS eprimer32 wrapper. For example, an extremely
> useful option will be: "SEQUENCE_PRIMER_PAIR_OK_REGION_LIST=,,2950,50",
> which I am not sure how to address, especially in Python. Any suggestion
> how to turn this option on or any other additional argument for Primer3
> through eprimer32 interface?

Tricky. This option has a specific format, with start positions and 
lengths as the values. Values are in groups of 4, but there can be 
multiple groups. EMBOSS deliberately makes these kinds of options hard 
to define because they make web interfaces complicated.

Primer3 also has a web interface so we can check how they handle this 
option.... and they simply allow users to type in a string!

We can do a little better, as we can read in the values as ranges and 
convert to start and length values when we write the options for primer3.

For this option, which needs a pair of ranges, we can try adding two 
sets of ranges - one for the left and one for the right, and combine 
them when setting the option with any missing values defaulting to empty.

We may also be able to improve our handling of ranges for eprimer32. We 
require start,end to be specified because that is the EMBOSS style, but 
perhaps we can extend the syntax to allow start,+len or start+len for 
any range in EMBOSS. This seems to be an easy change to make.

I will try a few options and look to add something to the next release.

regards,

Peter Rice
EMBOSS Team

From asidhu at biomap.org  Wed Oct 17 01:10:24 2012
From: asidhu at biomap.org (Amandeep Sidhu)
Date: Wed, 17 Oct 2012 13:10:24 +0800
Subject: [EMBOSS] International Symposium on Biomedical Data Infrastructure
	(BDI 2013)
Message-ID: <CAG_VK1T=UdR_MJjdXK31Pcm-GRDZOHi8rjX1Z_OM4rxxytX2qQ@mail.gmail.com>

International Symposium on Biomedical Data Infrastructure (BDI 2013)

30 - 31 January 2013

Kuala Lumpur, Malaysia

http://umconference.um.edu.my/BDI2013

Proceedings to be published by Springer

Due to the emerging demands of huge amounts of biomedical data, new and
improved data management capabilities are required for supporting a wide
range of applications. Current Biomedical Databases are independently
administered in geographically distinct locations, lending them almost
ideally to adoption of intelligent data management approaches. As a result
next generation of information infrastructure and data integration
capabilities are needed to ensure increasing infrastructure agility
required for high-throughput biomedical research. The workshop will focus
on research issues, problems and opportunities in Biomedical Data
Infrastructure.

Topics of Interest are:

* Big Biomedical Data and its Management
* Biomedical Data integration and Interoperability
* Next Generation Sequencing Data
* Biomedical Image Analysis
* Medical Informatics and Translational Bioinformatics
* Biomedical Ontologies
* Semantic Web Tools and Techniques for Biomedicine
* Web 2.0 and Web 3.0 Applications in Biomedicine
* Novel architectural models for HPC and cloud computing in Biomedicine
* New parallel / concurrent programming models for High Performance
Biomedical Applications in Cloud
* Biomedical Data Cloud
* Interoperability between different Utility Computing Platforms used for
Biomedicine
* Performance monitoring for biomedical applications in HPC and Cloud
* Biomedical Infrastructure as a Service
* Biomedical Platforms as a Service
* Biomedical Software as a Service
* Scientific workflows in bioinformatics and biomedicine
* Data Mining in Biomedicine
* Computational Systems Biology

Submission Guidelines:

We welcome original submissions that have not been published and that are
not under review by another conference or journal.  Papers should not
exceed 15 pages excluding references in Springer format. Paper should be
submitted through Easy Chair Online Submission System following
instructions on the website (http://umconference.um.edu.my/BDI2013). All
submissions will be evaluated on their originality, technical soundness,
significance, presentation, and interest to the symposium attendees.
Submission implies the willingness of at least one of the authors to
register and present the work associated with the paper submitted. All
submitted papers will be reviewed by symposium's technical program
committee. All accepted papers of registered authors will be included in
the proceedings published by Springer. All accepted papers will be required
to submit a Springer Copyright Form.

Important Dates:

Paper submission:               20 November 2012

Notifications sent to authors:  10 December 2012

Camera-ready papers due:        24 December 2012

Registration due:               10 January 2013

Conference:                     30 - 31 January 2013

Organizing Chairs:

Dr. Amandeep S. Sidhu (Curtin Sarawak Malaysia, Malaysia)
Dr. Sarinder Kaur (University of Malaya, Malaysia)

Steering Committee:

Dr. Dickson Lukose (MIMOS, Malaysia)
Dr. Kanagasabai Rajaraman (Institute for Infocomm Research, Singapore)
Prof. Dr. Meena Kishore Sakharkar (University of Tsukuba, Japan)
Prof. Dr. Jake Chen (Indiana University-Purdue University Indianapolis,
USA)
Prof. Dr. Xiaohua Tony Hu (Drexel University, USA)
Prof. Dr. Jason Tsong-Li Wang (New Jersey Institute of Technology, USA)
Prof. Dr. Carolyn McGregor (Health Informatics Research, Canada)

Please contact BDI 2013 Secretariat through email bdi at biomap.org for any
queries.

From aengus.stewart at cancer.org.uk  Thu Oct 18 10:52:44 2012
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Thu, 18 Oct 2012 15:52:44 +0100
Subject: [EMBOSS] Help to build a motif for fzzpro
In-Reply-To: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
References: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
Message-ID: <508017BC.80002@cancer.org.uk>

Hi all,

I have been asked to build a motif and the first part of the motif is.....

"The first 4 AAs must not be acidic and 1 of them should be basic"

I am not sure how to do this. So far I have

{DE}(4)

I am thinking I run with this and then post-filter the fuzzpro file?


Any ideas greatfully accepted.


Cheers
Aengus


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Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

From josef.maier at istls.de  Fri Oct 19 05:33:28 2012
From: josef.maier at istls.de (Dr. Josef Maier - IStLS)
Date: Fri, 19 Oct 2012 11:33:28 +0200
Subject: [EMBOSS] Help to build a motif for fzzpro
In-Reply-To: <mailman.9.1350576012.14868.emboss@lists.open-bio.org>
References: <mailman.9.1350576012.14868.emboss@lists.open-bio.org>
Message-ID: <50811E68.32039.7DB5B3@josef.maier.istls.de>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/emboss/attachments/20121019/f5d6aa26/attachment.html>

From gbottu at vub.ac.be  Fri Oct 19 05:55:22 2012
From: gbottu at vub.ac.be (Guy Bottu)
Date: Fri, 19 Oct 2012 11:55:22 +0200
Subject: [EMBOSS] Help to build a motif for fzzpro
In-Reply-To: <508017BC.80002@cancer.org.uk>
References: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
	<508017BC.80002@cancer.org.uk>
Message-ID: <5081238A.6010509@vub.ac.be>

	Dear Aengus,

I have an idea of how to do it. You must of course complete the 
motif/pattern as much as possible because with just {DE}(4) you will 
find much to much unless you search only a few sequences. You must run 
the program fuzzpro with parameter -rformat=listfile. You will obtain as 
output an EMBOSS list file. You can then run fuzzpro again with as 
sequence input list::xxx (xxx the name of your file) and as pattern 
input @yyy where yyy contains :

 > basic_1
<[HKR].
 > basic_2
<x-[HKR].
 > basic_3
<x-x-[HKR].
 > basic_4
<x-x-x-[HKR].

Indeed, the input will contain only sequence fragments matching the 
pattern and the basic amino acid hence should be in one of the first 4 
positions.

	Regards,
	Guy Bottu,
	ex-collaborator of the Belgian EMBnet Node

From ricepeterm at yahoo.co.uk  Fri Oct 19 06:26:56 2012
From: ricepeterm at yahoo.co.uk (Peter Rice)
Date: Fri, 19 Oct 2012 11:26:56 +0100
Subject: [EMBOSS] Help to build a motif for fzzpro
In-Reply-To: <50811E68.32039.7DB5B3@josef.maier.istls.de>
References: <mailman.9.1350576012.14868.emboss@lists.open-bio.org>
	<50811E68.32039.7DB5B3@josef.maier.istls.de>
Message-ID: <50812AF0.3040202@yahoo.co.uk>

On 19/10/2012 10:33, Dr. Josef Maier - IStLS wrote:
> Hello Angus,
>
> you could use preg with following pattern as written in regular
> expressions:
> ([KRH][^DE][^DE][^DE])|([^DE][KRH][^DE][^DE])|([^DE][^DE][KRH][^DE])|([^DE][^DE][^DE][KRH])
>
> Alternatively you could search with four different PROSITE-style
> patterns using fuzzpro and combine the result tables:
> [KRH]{DE}(3)
> {DE}(1)[KRH]{DE}(2)
> {DE}(2)[KRH]{DE}(1)
> [KRH]{DE}(3)

You can also put the four patterns in a file and use the syntax -pattern 
@patternfile

% cat patternfile
 >first
[KRH]{DE}(3)
 >second
{DE}(1)[KRH]{DE}(2)
 >third
{DE}(2)[KRH]{DE}(1)
 >fourth
[KRH]{DE}(3)

> For searching with combinations of PROSITE patterns, amino acid
> compositions and eventually AAINDEX profiles we had made a free web
> application for the University of Oslo, the SAPA tool:
> http://sapa-tool.uio.no/sapa/index.php

Interesting. I'll take a look.

> E.g. searching a 4-letter subsequence with the PROSITE-style patterns
> "[KRH].{DE}(4)", where the dot operator means logical AND, will produce
> a list of all subsequences having the two patterns in that application.
>
> Maybe the possibility to combine more than one PROSITE-style pattern
> within a fuzzpro search with logical AND would be a useful extension for
> fuzzpro improvement. Often more than one pattern is given for a domain
> or functional site in the PROSITE pattern database. Of course preg will
> do the job, however, the PROSITE patterns have to be rewritten as
> regular expressions.

We also have a long standing offer to revive scrutineer, written by 
Peter Sibbald at EMBL some years ago but it would need translation from 
Pascal (not too hard to do). It loaded SwissProt into memory and had 
interesting ways to search for motif patterns.

regards,

Peter Rice
EMBOSS Team


From daniel.rozenbaum at USPTO.GOV  Thu Oct 25 14:49:15 2012
From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc))
Date: Thu, 25 Oct 2012 14:49:15 -0400
Subject: [EMBOSS] changing default parameter values in Jemboss
Message-ID: <DBE16BB60D08774ABFD9473DD60A73D35B649E23@EMAIL02.uspto.gov>

Dear all,

Is there a way to adjust Jemboss so that, for example, the output section option "Full USA" of all applications where it's relevant (e.g. fuzznuc) is checked by default? I was able to tweak default values of those parameters that appear in the ACD files, but what about those that are not explicitly mentioned on the ACD file?

Many thanks,
Daniel

--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/ Office of Application Engineering&   Development/ Patent System Division
600 Dulany St., Alexandria, VA 22314



From daniel.rozenbaum at USPTO.GOV  Tue Oct  2 15:02:57 2012
From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc))
Date: Tue, 2 Oct 2012 11:02:57 -0400
Subject: [EMBOSS] fuzzpro memory consumption
Message-ID: <DBE16BB60D08774ABFD9473DD60A73D350D697AE@EMAIL02.uspto.gov>

Dear all,

We attempted to run a fuzzpro search of the UniProt database with the following pattern:

[LIVMSTAC]-[LIVMFYWSTAGC]-[LIMSTAG]-[LIVMSTAGC]-x(2)-[DN]-x-{P}- [LIVMWSTAC]-{DP}-[LIVMFSTAG]-W-[DEN]-[LIVMFSTAGCN]

The job appears to have brought the server into a hung state, and my best guess is that the process consumed so much memory that it caused heavy swapping.

I'm still not 100% sure that my assumption is correct, but in any event, is there a way to gauge how much memory will a fuzznuc/pro or dreg/preg job consume, based on the complexity of the pattern, size of the database, expected number of matches, etc?

Many thanks,
Daniel

--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/Office of Application Engineering & Development/Patent System Division
600 Dulany St.
Alexandria, VA 22314




From daniel.rozenbaum at USPTO.GOV  Fri Oct 12 21:27:56 2012
From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc))
Date: Fri, 12 Oct 2012 17:27:56 -0400
Subject: [EMBOSS] Space in USA "db:seqname" in list file causes unintended
	behavior
Message-ID: <DBE16BB60D08774ABFD9473DD60A73D350D6982F@EMAIL02.uspto.gov>

Hello everyone,

We have encountered the following issue: if there's an erroneous (most likely unintentionally) entry in a list file that looks like "db:<space character>seqname", EMBOSS doesn't issue an error/warning message, but treats this entry as "db:*". Here's an example using the test database tsw in EMBOSS distribution; it contains 100 sequences, three of which match the pattern "hba*" :

% seqret tsw -auto -stdout  | egrep "^>" | wc -l
100
% cat list2
tsw:hba*
% seqret list::list2 -auto -stdout  | egrep "^>" | wc -l
3
% cat list1
tsw: hba*
% seqret list::list1 -auto -stdout  | egrep "^>" | wc -l
100
Of course, the immediate answer is to instruct the users to be careful not to allow unintended spaces in the USA's. Might it be possible though to add some protection against potentially problematic consequences if such an error in the USA is made? In one such instance the resultant clustalw process ended up attempting to build a multiple alignment across the entire UniProt, which the server didn't handle well :-)

With best regards,
Daniel

--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/ Office of Application Engineering & Development/ Patent System Division
600 Dulany St.
Alexandria, VA 22314



From ricepeterm at yahoo.co.uk  Sat Oct 13 07:40:15 2012
From: ricepeterm at yahoo.co.uk (Peter Rice)
Date: Sat, 13 Oct 2012 08:40:15 +0100
Subject: [EMBOSS] Space in USA "db:seqname" in list file causes
 unintended behavior
In-Reply-To: <DBE16BB60D08774ABFD9473DD60A73D350D6982F@EMAIL02.uspto.gov>
References: <DBE16BB60D08774ABFD9473DD60A73D350D6982F@EMAIL02.uspto.gov>
Message-ID: <50791ADF.1040608@yahoo.co.uk>

On 12/10/2012 22:27, Rozenbaum, Daniel (Biocceleration Inc) wrote:
> Hello everyone,
>
> We have encountered the following issue: if there's an erroneous (most likely unintentionally) entry in a list file that looks like "db:<space character>seqname", EMBOSS doesn't issue an error/warning message, but treats this entry as "db:*". >
>
> Might it be possible though to add some protection against potentially problematic consequences if such an error in the USA is made? In one such instance the resultant clustalw process ended up attempting to build a multiple alignment across the entire UniProt, which the server didn't handle well :-)

An interesting problem. List files have a long history, going back 
before EMBOSS. They were also used in the GCG (Wisconsin) package, which 
in turn adopted them from the VMS operating system. where they could be 
used for mailing lists (sending to @list with a list of usernames, for 
example).

In a list file, only the first token (word) is significant. The 
remainder of the line is treated as a comment.

As you discovered, a space before the id (or indeed just a database 
name) is a valid input representing all entries in the database.

I think it is safe to assume that list files in practice have no 
comments, so we can make a simple change for the next release:

list:: indicates a list file with only one token per line. Any 
extraneous text will result in an error or warning message

The same restriction will be applied to the VMS syntax @listfile

A new list style can be added to allow comments so that any user with 
them can still use their list files.

Possibly a stricter comment style could be allowed in standard list:: 
files. We can check what other packages may have introduced, but 
something like a perl-style #comment could be simple to add. The # 
character has no special meaning in the EMBOSS query language.

With those changes in place your users would be saved from extra spaces 
... but of course would still be caught by a newline creeping in to 
start a new record after the database name (reading the entire database, 
then reading the id as a possible filename). Users will get an error 
message from that so long as the second part is not a valid filename or 
database name.

regards,

Peter Rice
EMBOSS Team




From ivaylo.stoimenov at gmail.com  Mon Oct 15 12:03:27 2012
From: ivaylo.stoimenov at gmail.com (Ivaylo Stoimenov)
Date: Mon, 15 Oct 2012 14:03:27 +0200
Subject: [EMBOSS] EMBOSS/Primer3
Message-ID: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>

Hi,

I am wondering if it is possible to pass some of the newest options to
Primer 3, through EMBOSS eprimer32 wrapper. For example, an extremely
useful option will be: "SEQUENCE_PRIMER_PAIR_OK_REGION_LIST=,,2950,50",
which I am not sure how to address, especially in Python. Any suggestion
how to turn this option on or any other additional argument for Primer3
through eprimer32 interface?

Reagrds,
Ivaylo


From ricepeterm at yahoo.co.uk  Mon Oct 15 14:00:33 2012
From: ricepeterm at yahoo.co.uk (Peter Rice)
Date: Mon, 15 Oct 2012 15:00:33 +0100
Subject: [EMBOSS] EMBOSS/Primer3
In-Reply-To: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
References: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
Message-ID: <507C1701.9040403@yahoo.co.uk>

On 15/10/2012 13:03, Ivaylo Stoimenov wrote:
> Hi,
>
> I am wondering if it is possible to pass some of the newest options to
> Primer 3, through EMBOSS eprimer32 wrapper. For example, an extremely
> useful option will be: "SEQUENCE_PRIMER_PAIR_OK_REGION_LIST=,,2950,50",
> which I am not sure how to address, especially in Python. Any suggestion
> how to turn this option on or any other additional argument for Primer3
> through eprimer32 interface?

Tricky. This option has a specific format, with start positions and 
lengths as the values. Values are in groups of 4, but there can be 
multiple groups. EMBOSS deliberately makes these kinds of options hard 
to define because they make web interfaces complicated.

Primer3 also has a web interface so we can check how they handle this 
option.... and they simply allow users to type in a string!

We can do a little better, as we can read in the values as ranges and 
convert to start and length values when we write the options for primer3.

For this option, which needs a pair of ranges, we can try adding two 
sets of ranges - one for the left and one for the right, and combine 
them when setting the option with any missing values defaulting to empty.

We may also be able to improve our handling of ranges for eprimer32. We 
require start,end to be specified because that is the EMBOSS style, but 
perhaps we can extend the syntax to allow start,+len or start+len for 
any range in EMBOSS. This seems to be an easy change to make.

I will try a few options and look to add something to the next release.

regards,

Peter Rice
EMBOSS Team


From asidhu at biomap.org  Wed Oct 17 05:10:24 2012
From: asidhu at biomap.org (Amandeep Sidhu)
Date: Wed, 17 Oct 2012 13:10:24 +0800
Subject: [EMBOSS] International Symposium on Biomedical Data Infrastructure
	(BDI 2013)
Message-ID: <CAG_VK1T=UdR_MJjdXK31Pcm-GRDZOHi8rjX1Z_OM4rxxytX2qQ@mail.gmail.com>

International Symposium on Biomedical Data Infrastructure (BDI 2013)

30 - 31 January 2013

Kuala Lumpur, Malaysia

http://umconference.um.edu.my/BDI2013

Proceedings to be published by Springer

Due to the emerging demands of huge amounts of biomedical data, new and
improved data management capabilities are required for supporting a wide
range of applications. Current Biomedical Databases are independently
administered in geographically distinct locations, lending them almost
ideally to adoption of intelligent data management approaches. As a result
next generation of information infrastructure and data integration
capabilities are needed to ensure increasing infrastructure agility
required for high-throughput biomedical research. The workshop will focus
on research issues, problems and opportunities in Biomedical Data
Infrastructure.

Topics of Interest are:

* Big Biomedical Data and its Management
* Biomedical Data integration and Interoperability
* Next Generation Sequencing Data
* Biomedical Image Analysis
* Medical Informatics and Translational Bioinformatics
* Biomedical Ontologies
* Semantic Web Tools and Techniques for Biomedicine
* Web 2.0 and Web 3.0 Applications in Biomedicine
* Novel architectural models for HPC and cloud computing in Biomedicine
* New parallel / concurrent programming models for High Performance
Biomedical Applications in Cloud
* Biomedical Data Cloud
* Interoperability between different Utility Computing Platforms used for
Biomedicine
* Performance monitoring for biomedical applications in HPC and Cloud
* Biomedical Infrastructure as a Service
* Biomedical Platforms as a Service
* Biomedical Software as a Service
* Scientific workflows in bioinformatics and biomedicine
* Data Mining in Biomedicine
* Computational Systems Biology

Submission Guidelines:

We welcome original submissions that have not been published and that are
not under review by another conference or journal.  Papers should not
exceed 15 pages excluding references in Springer format. Paper should be
submitted through Easy Chair Online Submission System following
instructions on the website (http://umconference.um.edu.my/BDI2013). All
submissions will be evaluated on their originality, technical soundness,
significance, presentation, and interest to the symposium attendees.
Submission implies the willingness of at least one of the authors to
register and present the work associated with the paper submitted. All
submitted papers will be reviewed by symposium's technical program
committee. All accepted papers of registered authors will be included in
the proceedings published by Springer. All accepted papers will be required
to submit a Springer Copyright Form.

Important Dates:

Paper submission:               20 November 2012

Notifications sent to authors:  10 December 2012

Camera-ready papers due:        24 December 2012

Registration due:               10 January 2013

Conference:                     30 - 31 January 2013

Organizing Chairs:

Dr. Amandeep S. Sidhu (Curtin Sarawak Malaysia, Malaysia)
Dr. Sarinder Kaur (University of Malaya, Malaysia)

Steering Committee:

Dr. Dickson Lukose (MIMOS, Malaysia)
Dr. Kanagasabai Rajaraman (Institute for Infocomm Research, Singapore)
Prof. Dr. Meena Kishore Sakharkar (University of Tsukuba, Japan)
Prof. Dr. Jake Chen (Indiana University-Purdue University Indianapolis,
USA)
Prof. Dr. Xiaohua Tony Hu (Drexel University, USA)
Prof. Dr. Jason Tsong-Li Wang (New Jersey Institute of Technology, USA)
Prof. Dr. Carolyn McGregor (Health Informatics Research, Canada)

Please contact BDI 2013 Secretariat through email bdi at biomap.org for any
queries.


From aengus.stewart at cancer.org.uk  Thu Oct 18 14:52:44 2012
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Thu, 18 Oct 2012 15:52:44 +0100
Subject: [EMBOSS] Help to build a motif for fzzpro
In-Reply-To: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
References: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
Message-ID: <508017BC.80002@cancer.org.uk>

Hi all,

I have been asked to build a motif and the first part of the motif is.....

"The first 4 AAs must not be acidic and 1 of them should be basic"

I am not sure how to do this. So far I have

{DE}(4)

I am thinking I run with this and then post-filter the fuzzpro file?


Any ideas greatfully accepted.


Cheers
Aengus


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From josef.maier at istls.de  Fri Oct 19 09:33:28 2012
From: josef.maier at istls.de (Dr. Josef Maier - IStLS)
Date: Fri, 19 Oct 2012 11:33:28 +0200
Subject: [EMBOSS] Help to build a motif for fzzpro
In-Reply-To: <mailman.9.1350576012.14868.emboss@lists.open-bio.org>
References: <mailman.9.1350576012.14868.emboss@lists.open-bio.org>
Message-ID: <50811E68.32039.7DB5B3@josef.maier.istls.de>

An HTML attachment was scrubbed...
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From gbottu at vub.ac.be  Fri Oct 19 09:55:22 2012
From: gbottu at vub.ac.be (Guy Bottu)
Date: Fri, 19 Oct 2012 11:55:22 +0200
Subject: [EMBOSS] Help to build a motif for fzzpro
In-Reply-To: <508017BC.80002@cancer.org.uk>
References: <CA+q_Z7KHZttmeWCVjd13JWdfOb51TmgQAfGxaybAbs6LETe1mw@mail.gmail.com>
	<508017BC.80002@cancer.org.uk>
Message-ID: <5081238A.6010509@vub.ac.be>

	Dear Aengus,

I have an idea of how to do it. You must of course complete the 
motif/pattern as much as possible because with just {DE}(4) you will 
find much to much unless you search only a few sequences. You must run 
the program fuzzpro with parameter -rformat=listfile. You will obtain as 
output an EMBOSS list file. You can then run fuzzpro again with as 
sequence input list::xxx (xxx the name of your file) and as pattern 
input @yyy where yyy contains :

 > basic_1
<[HKR].
 > basic_2
<x-[HKR].
 > basic_3
<x-x-[HKR].
 > basic_4
<x-x-x-[HKR].

Indeed, the input will contain only sequence fragments matching the 
pattern and the basic amino acid hence should be in one of the first 4 
positions.

	Regards,
	Guy Bottu,
	ex-collaborator of the Belgian EMBnet Node


From ricepeterm at yahoo.co.uk  Fri Oct 19 10:26:56 2012
From: ricepeterm at yahoo.co.uk (Peter Rice)
Date: Fri, 19 Oct 2012 11:26:56 +0100
Subject: [EMBOSS] Help to build a motif for fzzpro
In-Reply-To: <50811E68.32039.7DB5B3@josef.maier.istls.de>
References: <mailman.9.1350576012.14868.emboss@lists.open-bio.org>
	<50811E68.32039.7DB5B3@josef.maier.istls.de>
Message-ID: <50812AF0.3040202@yahoo.co.uk>

On 19/10/2012 10:33, Dr. Josef Maier - IStLS wrote:
> Hello Angus,
>
> you could use preg with following pattern as written in regular
> expressions:
> ([KRH][^DE][^DE][^DE])|([^DE][KRH][^DE][^DE])|([^DE][^DE][KRH][^DE])|([^DE][^DE][^DE][KRH])
>
> Alternatively you could search with four different PROSITE-style
> patterns using fuzzpro and combine the result tables:
> [KRH]{DE}(3)
> {DE}(1)[KRH]{DE}(2)
> {DE}(2)[KRH]{DE}(1)
> [KRH]{DE}(3)

You can also put the four patterns in a file and use the syntax -pattern 
@patternfile

% cat patternfile
 >first
[KRH]{DE}(3)
 >second
{DE}(1)[KRH]{DE}(2)
 >third
{DE}(2)[KRH]{DE}(1)
 >fourth
[KRH]{DE}(3)

> For searching with combinations of PROSITE patterns, amino acid
> compositions and eventually AAINDEX profiles we had made a free web
> application for the University of Oslo, the SAPA tool:
> http://sapa-tool.uio.no/sapa/index.php

Interesting. I'll take a look.

> E.g. searching a 4-letter subsequence with the PROSITE-style patterns
> "[KRH].{DE}(4)", where the dot operator means logical AND, will produce
> a list of all subsequences having the two patterns in that application.
>
> Maybe the possibility to combine more than one PROSITE-style pattern
> within a fuzzpro search with logical AND would be a useful extension for
> fuzzpro improvement. Often more than one pattern is given for a domain
> or functional site in the PROSITE pattern database. Of course preg will
> do the job, however, the PROSITE patterns have to be rewritten as
> regular expressions.

We also have a long standing offer to revive scrutineer, written by 
Peter Sibbald at EMBL some years ago but it would need translation from 
Pascal (not too hard to do). It loaded SwissProt into memory and had 
interesting ways to search for motif patterns.

regards,

Peter Rice
EMBOSS Team



From daniel.rozenbaum at USPTO.GOV  Thu Oct 25 18:49:15 2012
From: daniel.rozenbaum at USPTO.GOV (Rozenbaum, Daniel (Biocceleration Inc))
Date: Thu, 25 Oct 2012 14:49:15 -0400
Subject: [EMBOSS] changing default parameter values in Jemboss
Message-ID: <DBE16BB60D08774ABFD9473DD60A73D35B649E23@EMAIL02.uspto.gov>

Dear all,

Is there a way to adjust Jemboss so that, for example, the output section option "Full USA" of all applications where it's relevant (e.g. fuzznuc) is checked by default? I was able to tweak default values of those parameters that appear in the ACD files, but what about those that are not explicitly mentioned on the ACD file?

Many thanks,
Daniel

--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/ Office of Application Engineering&   Development/ Patent System Division
600 Dulany St., Alexandria, VA 22314