[Biojava-l] Can BioJava do Multiple Alignments?
mark.schreiber at novartis.com
mark.schreiber at novartis.com
Thu Nov 2 06:03:13 UTC 2006
In short -- No.
The best solution is probably to call ClustalW in a process. You could of
course reimplement the algorithm in biojava if you wish. The DP library
could also be extended for MSA but this would be hard work.
- Mark
Mark Schreiber
Research Investigator (Bioinformatics)
Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org
phone +65 6722 2973
fax +65 6722 2910
"Michael Tran" <michael.tran at acpfg.com.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/02/2006 01:43 PM
To: <biojava-l at lists.open-bio.org>
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Can BioJava do Multiple Alignments?
<http://www.acpfg.com.au/profiles/Michael_Tran.html>
Hi,
I know that BioJava 1.5 can do pairwise alignments using algorithms like
SmithWaterman and NeedlemanWunch. But can BioJava do multiple alignments
like the algorthm used for ClustalW? I have also checked the HMM classes,
but they appear to only do pairwise alignments.
Michael
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Today's Topics:
1. Re: can BioJava do alignment ? (Ramon Medrado)
2. Re: can BioJava do alignment ? (mark.schreiber at novartis.com)
3. More extensive Bioperl-run 1.5.2RC2 tests (Nathan S. Haigh)
4. Re: More extensive Bioperl-run 1.5.2RC2 tests (Nathan Haigh)
5. fasta description line (ThorstenInAnger)
6. pK values (Gerster Sarah)
7. Re: fasta description line (Mark Schreiber)
8. Re: pK values (Mark Schreiber)
9. Re: pK values (David Huen)
10. Using Java to create BLAST searches (Graham Etherington)
----------------------------------------------------------------------
Message: 1
Date: Thu, 19 Oct 2006 14:45:24 -0300
From: "Ramon Medrado" <rmedrado at gmail.com>
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
<37ba4b050610191045q30a6282bjce052e31e1463cea at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi,
The information is true. Biojava 1.5 has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz
and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar
and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz
I wait to have helped
--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil
2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it
can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that BioJava 1.5 can do alignment itself (e.g.,
I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
> is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
> itself ?
if it does, I downloaded the CVS view of BioJava 1.5, but could not
find
> any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
------------------------------
Message: 2
Date: Fri, 20 Oct 2006 09:57:09 +0800
From: mark.schreiber at novartis.com
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: "Ramon Medrado" <rmedrado at gmail.com>, CARMELK at il.ibm.com
Cc: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
<OFED374D90.C3E37FD4-ON4825720D.000A9274-4825720D.000AB9F8 at ah.novartis.com>
Content-Type: text/plain; charset="us-ascii"
Hi -
You can also perform an alignment using HMMs in biojava 1.3 and 1.4. See
the example at (http://biojava.org/wiki/BioJava:CookBook:DP:PairWise).
This is actually the most flexible way to do it.
- Mark
Mark Schreiber
Research Investigator (Bioinformatics)
Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org
phone +65 6722 2973
fax +65 6722 2910
"Ramon Medrado" <rmedrado at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
10/20/2006 01:45 AM
To: biojava <Biojava-l at lists.open-bio.org>
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: Re: [Biojava-l] can BioJava do alignment ?
Hi,
The information is true. Biojava 1.5 has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz
and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar
and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz
I wait to have helped
--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil
2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it
can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that BioJava 1.5 can do alignment itself (e.g.,
I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
> is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
> itself ?
if it does, I downloaded the CVS view of BioJava 1.5, but could not
find
> any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
_______________________________________________
Biojava-l mailing list - Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l
------------------------------
Message: 3
Date: Wed, 25 Oct 2006 13:54:26 +0000
From: "Nathan S. Haigh" <n.haigh at sheffield.ac.uk>
Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <453F6C92.6020207 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1
I have recently installed some more software for which there are
bioperl-run tests and run the test suite with several versions of the
software I could find. I've added info to
http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
fails in any of the versions I tested I've noted them together with
versions that were ok (if any).
There maybe another 6 or so programs I'm trying to get hold of to run
further tests - I'll update when I get them.
Nath
------------------------------
Message: 4
Date: Thu, 26 Oct 2006 09:46:13 +0100
From: Nathan Haigh <n.haigh at sheffield.ac.uk>
Subject: Re: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <454075D5.2030005 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1
Nathan S. Haigh wrote:
> I have recently installed some more software for which there are
> bioperl-run tests and run the test suite with several versions of the
> software I could find. I've added info to
> http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
> fails in any of the versions I tested I've noted them together with
> versions that were ok (if any).
>
> There maybe another 6 or so programs I'm trying to get hold of to run
> further tests - I'll update when I get them.
> Nath
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
My aplogies, this should have gone to the Bioperl mailing list! :o)
------------------------------
Message: 5
Date: Mon, 23 Oct 2006 02:57:14 -0700 (PDT)
From: ThorstenInAnger <henrich at embl.de>
Subject: [Biojava-l] fasta description line
To: biojava-l at lists.open-bio.org
Message-ID: <6950970.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii
Hi,
I want to do something very simple:
- get id and sequence from a database
- create a sequence object
- write it out as fasta format file (with a defined description line)
this is my code:
rs = stmt.executeQuery(query);
Feature.Template templ = new
Feature.Template();
//fill in the template
Annotation an = new SimpleAnnotation();
templ.location = Location.empty;
while (rs.next()) {
mepdId = rs.getInt(1);
mepdName = rs.getString(2);
seq = rs.getString(3);
seqObj =
DNATools.createDNASequence(seq, mepdName);
an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
here");
templ.annotation = an;
seqObj.createFeature(templ);
SeqIOTools.writeFasta(fastaFos,
seqObj);
//db.addSequence(seqObj);
}
It works fine, but there is no description line in the resulting file!
How can I change the fasta description line?
Also I am using deprecated methods, but could not find out what to use
instead:
FastaFormat.PROPERTY_DESCRIPTIONLINE
SeqIOTools.writeFasta
All tutorials I found are using the deprecated.
Cheers,
Thorsten
--
View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
Sent from the BioJava mailing list archive at Nabble.com.
------------------------------
Message: 6
Date: Tue, 31 Oct 2006 09:04:33 +0100
From: "Gerster Sarah" <sgerster at student.ethz.ch>
Subject: [Biojava-l] pK values
To: <biojava-l at lists.open-bio.org>
Message-ID: <E9D421793368D44FB81D3C438D300574BC729D at EX5.d.ethz.ch>
Content-Type: text/plain; charset="iso-8859-1"
Hi!
I want to compute the pI of some sequences. I looked at
"IsoelectricPointCalc.java". Where do the values for the pks come from?
are they defined as constants somewhere? I couldn't find them... I wanted
to see if the values are the same ones than the ones that I am supposed to
use.
And another question> reading in sequences from an xml file... Is there
something that I can use, or do I have to write it on my own?
Cheers
Sarah
------------------------------
Message: 7
Date: Tue, 31 Oct 2006 17:37:24 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] fasta description line
To: ThorstenInAnger <henrich at embl.de>
Cc: biojava-l at lists.open-bio.org
Message-ID:
<93b45ca50610310137u68700b06se364f99da69feb47 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi -
If you are using biojava 1.5 beta (recommended) you should use
RichSequence.IOTools to write the fasta (strongly recommended).
With the new org.biojavax.bio.seq.io.FastaFormat object the
description line is constructed from:
richSequence.getIdentifier()
richSequence.getNamespace().getName();
richSequence.getAccession()
richSequence.getVersion()
richSequence.getName()
richSequence.getDescription()
- Mark
On 10/23/06, ThorstenInAnger <henrich at embl.de> wrote:
>
> Hi,
>
> I want to do something very simple:
>
> - get id and sequence from a database
> - create a sequence object
> - write it out as fasta format file (with a defined description line)
>
> this is my code:
> rs = stmt.executeQuery(query);
> Feature.Template templ = new
Feature.Template();
>
> //fill in the template
> Annotation an = new SimpleAnnotation();
> templ.location = Location.empty;
>
> while (rs.next()) {
> mepdId = rs.getInt(1);
> mepdName = rs.getString(2);
> seq = rs.getString(3);
> seqObj =
DNATools.createDNASequence(seq, mepdName);
> an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
> here");
> templ.annotation = an;
> seqObj.createFeature(templ);
> SeqIOTools.writeFasta(fastaFos,
seqObj);
> //db.addSequence(seqObj);
> }
>
> It works fine, but there is no description line in the resulting file!
> How can I change the fasta description line?
>
> Also I am using deprecated methods, but could not find out what to use
> instead:
> FastaFormat.PROPERTY_DESCRIPTIONLINE
> SeqIOTools.writeFasta
> All tutorials I found are using the deprecated.
>
> Cheers,
>
> Thorsten
>
> --
> View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
> Sent from the BioJava mailing list archive at Nabble.com.
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
------------------------------
Message: 8
Date: Tue, 31 Oct 2006 17:27:29 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] pK values
To: "Gerster Sarah" <sgerster at student.ethz.ch>
Cc: biojava-l at lists.open-bio.org
Message-ID:
<93b45ca50610310127h75010e56ne31e188294e23803 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi -
The values are calculated using the SymbolPropertyTable returned by
ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);
This table gets it's values from the resource file
org/biojava/bio/symbol/ResidueProperties.xml
The pK values were added by david huen (I think).
To read XML sequence files try one of the methods in
RichSequence.IOTools from biojava 1.5 beta.
- Mark
On 10/31/06, Gerster Sarah <sgerster at student.ethz.ch> wrote:
> Hi!
>
> I want to compute the pI of some sequences. I looked at
"IsoelectricPointCalc.java". Where do the values for the pks come from?
are they defined as constants somewhere? I couldn't find them... I wanted
to see if the values are the same ones than the ones that I am supposed to
use.
>
> And another question> reading in sequences from an xml file... Is there
something that I can use, or do I have to write it on my own?
>
> Cheers
>
> Sarah
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
------------------------------
Message: 9
Date: 31 Oct 2006 12:21:43 +0000
From: David Huen <smh1008 at cam.ac.uk>
Subject: Re: [Biojava-l] pK values
To: Mark Schreiber <markjschreiber at gmail.com>
Cc: biojava-l at lists.open-bio.org
Message-ID: <Prayer.1.0.18.0610311221430.32704 at hermes-1.csi.cam.ac.uk>
Content-Type: text/plain; format=flowed; charset=ISO-8859-1
On Oct 31 2006, Mark Schreiber wrote:
>Hi -
>
>The values are calculated using the SymbolPropertyTable returned by
>ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);
>
>This table gets it's values from the resource file
>org/biojava/bio/symbol/ResidueProperties.xml
>
>The pK values were added by david huen (I think).
>
I used the same pK values as those used by GCG to maintian
cross-compability.
Regards,
David
------------------------------
Message: 10
Date: Wed, 1 Nov 2006 18:39:24 +1000
From: "Graham Etherington" <g.etherington at imb.uq.edu.au>
Subject: [Biojava-l] Using Java to create BLAST searches
To: <biojava-l at lists.open-bio.org>
Message-ID: <008901c6fd91$3c415e40$36776682 at IMBPC.AD>
Content-Type: text/plain; charset="us-ascii"
Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error
when
I run my search, namely:
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "
The pertinent bits of code I'm using are...
String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";
............
Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
runBlast.waitFor ();
out.println ("Waiting for result");
//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);
.............
I'm not sure why it give me an IOException. I've checked that the file
input
file exists and that all the paths are correct.
Any ideas?
Many thanks,
Graham
------------------------------
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