<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
________________________________ From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Wed 1/11/2006 8:09 PM To: [email protected] Subject: Biojava-l Digest, Vol 47, Issue 1 Send Biojava-l mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://lists.open-bio.org/mailman/listinfo/biojava-l or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of Biojava-l digest..." Today's Topics: 1. Re: can BioJava do alignment ? (Ramon Medrado) 2. Re: can BioJava do alignment ? ([EMAIL PROTECTED]) 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" <[EMAIL PROTECTED]> Subject: Re: [Biojava-l] can BioJava do alignment ? To: biojava <[email protected]> Message-ID: <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>: > > > 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: [EMAIL PROTECTED] > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > ------------------------------ Message: 2 Date: Fri, 20 Oct 2006 09:57:09 +0800 From: [EMAIL PROTECTED] Subject: Re: [Biojava-l] can BioJava do alignment ? To: "Ramon Medrado" <[EMAIL PROTECTED]>, [EMAIL PROTECTED] Cc: biojava <[email protected]> Message-ID: <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 10/20/2006 01:45 AM To: biojava <[email protected]> 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 <[EMAIL PROTECTED]>: > > > 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: [EMAIL PROTECTED] > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l ------------------------------ Message: 3 Date: Wed, 25 Oct 2006 13:54:26 +0000 From: "Nathan S. Haigh" <[EMAIL PROTECTED]> Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests To: [email protected] Message-ID: <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> Subject: Re: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests To: [email protected] Message-ID: <[EMAIL PROTECTED]> 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 - [email protected] > 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 <[EMAIL PROTECTED]> Subject: [Biojava-l] fasta description line To: [email protected] Message-ID: <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> Subject: [Biojava-l] pK values To: <[email protected]> Message-ID: <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> Subject: Re: [Biojava-l] fasta description line To: ThorstenInAnger <[EMAIL PROTECTED]> Cc: [email protected] Message-ID: <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > ------------------------------ Message: 8 Date: Tue, 31 Oct 2006 17:27:29 +0800 From: "Mark Schreiber" <[EMAIL PROTECTED]> Subject: Re: [Biojava-l] pK values To: "Gerster Sarah" <[EMAIL PROTECTED]> Cc: [email protected] Message-ID: <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > ------------------------------ Message: 9 Date: 31 Oct 2006 12:21:43 +0000 From: David Huen <[EMAIL PROTECTED]> Subject: Re: [Biojava-l] pK values To: Mark Schreiber <[EMAIL PROTECTED]> Cc: [email protected] Message-ID: <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> Subject: [Biojava-l] Using Java to create BLAST searches To: <[email protected]> Message-ID: <[EMAIL PROTECTED]> 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 ------------------------------ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l End of Biojava-l Digest, Vol 47, Issue 1 **************************************** _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
