Hi Does anyone have any example code to digest proteins and work out the mass of the peptides generated?
[EMAIL PROTECTED] wrote: > > Send Biojava-l mailing list submissions to > [EMAIL PROTECTED] > > To subscribe or unsubscribe via the World Wide Web, visit > http://biojava.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: Best way to represent multiple annotation "tracks" > (Ihab A.B. Awad) > 2. Reformating multiple sequence alignments (Gabriel del Rio Guerra) > 3. Parsing location from gbk files > ( [EMAIL PROTECTED] ) > 4. RE: Reformating multiple sequence alignments (Schreiber, Mark) > 5. RE: Parsing location from gbk files (Schreiber, Mark) > 6. Re: Parsing location from gbk files (Matthew Pocock) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 8 Sep 2003 16:53:09 -0700 > From: "Ihab A.B. Awad" <[EMAIL PROTECTED]> > Subject: RE: [Biojava-l] Best way to represent multiple annotation > "tracks" > To: "Schreiber, Mark" <[EMAIL PROTECTED]>, > <[EMAIL PROTECTED]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="us-ascii" ; format="flowed" > > Hi again, > > [ Pls excuse the poor netiquette for posting a followup to my own message.... ] > > >So, let's say I have a bunch of ESTs, each of which has been mapped > >to a location on the genome. To each EST, my data maps a floating > >point number indicating the expression level. > > > >In this case, each Feature would represent one of the ESTs, right? > >So what would be the Feature(s) representing the annotation track? > >Would they be Features owned by the EST Feature (via the inheritance > >of FeatureHolder by interface Feature)? Or -- ?? > > Alternatively, would each EST be a SubSequence with Features attached > to it, with each Feature representing one of the data "tracks"? If > so, then how does one decide when something is a Feature or a > SubSequence? I'm not a biologist, so I'm probably way confused here, > but it seems to me there is a gray area (ORFs?). > > So I guess there are several competing implementations. > > 1. SEQUENCE BASED, FEATURES REPRESENT DATA TRACKS > > "Chromosome 1" : Sequence > "AA504327" : SubSequence > "RAT2N" : Feature > <anon> : Annotation > "Value" => 2.34312 > "RAT2_MEAN": Feature > <anon> : Annotation > "Value" => 1.8342 > "AA432030" : SubSequence > ... > > 2. SEQUENCE BASED, ANNOTATIONS REPRESENT DATA TRACKS > > "Chromosome 1" : Sequence > "AA504327" : SubSequence > "Microarray Experiment B2341v" : Feature > <anon> : Annotation > "RAT2N" => 2.34312 > "RAT2_MEAN" => 1.8342 > "AA432030" : SubSequence > ... > > 3. FEATURE BASED, SUB-FEATURES REPRESENT DATA TRACKS > > (Very similar to #1, except using Feature instead of SubSequence.) > > "Chromosome 1" : Sequence > "AA504327" : Feature > "RAT2N" : Feature > <anon> : Annotation > "Value" => 2.34312 > "RAT2_MEAN": Feature > <anon> : Annotation > "Value" => 1.8342 > "AA432030" : SubSequence > ... > > 4. FEATURE BASED, ANNOTATIONS REPRESENT DATA TRACKS > > (Very similar to #2, except using Feature instead of SubSequence.) > > "Chromosome 1" : Sequence > "AA504327" : Feature > "Microarray Experiment B2341v" : Feature > <anon> : Annotation > "RAT2N" => 2.34312 > "RAT2_MEAN" => 1.8342 > "AA432030" : SubSequence > ... > > Thanks a lot again & peace, > > Ihab > > -- > Ihab A.B. Awad <[EMAIL PROTECTED]> > Snr Scientific Programmer, Dept of Genetics > > ------------------------------ > > Message: 2 > Date: Wed, 10 Sep 2003 09:06:00 -0700 > From: "Gabriel del Rio Guerra" <[EMAIL PROTECTED]> > Subject: [Biojava-l] Reformating multiple sequence alignments > To: <[EMAIL PROTECTED]> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I am interesting in using or developing a program to inter-convert > different sequence alignments formats. In particular I want to translate > HSSP alignments into MSF format. Does anyone knows if this is possible > with Biojava at this point? > > Thanks, > > Gabriel > > -----Original Message----- > From: Kenny Yu [mailto:[EMAIL PROTECTED] > Sent: Wednesday, April 30, 2003 8:45 AM > To: [EMAIL PROTECTED] > Subject: [Biojava-l] unified consolidated annotation system > > Both biosql and biodas are concerned with retrieving annotation on the > basis of known features. They are not optimized for large-scale > cross-system queries and data mining on the basis of annotations. I am > interested in consolidating annotations from various sources (such as > genbank and unigene) into a unified form on which I can run queries like > "find features that are linked to DNA repair function in human but not > in mouse" and "find feature whose molecular functions overlap with > those of Accession Number nnnn". Similar mechanisms may exist in LION's > SRS (http://www.lionbioscience.com/solutions/products/srs/relational). > What I am contemplating is essentially a data warehouse for annotations. > I'll borrow data warehouse and OLAP techniques in the design. It's a > hybrid of relational, nested-relational and multidimensional database. > Feature entity, or gene, and annotation are the dimensions. It models > textual values as well as binary objects such as pathway diagrams as > annot! > ation values. I intend to make my work open-source and would call it > UCAsql. Currently the schema design, with some documentation and java > API, is available to anyone upon request by email to myself at > [EMAIL PROTECTED] > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > > ------------------------------ > > Message: 3 > Date: Wed, 10 Sep 2003 20:13:41 +0200 > From: " [EMAIL PROTECTED] " > <[EMAIL PROTECTED]> > Subject: [Biojava-l] Parsing location from gbk files > To: " biojava-l " <[EMAIL PROTECTED]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=iso-8859-1 > > Hi, > > I am using biojava to extract mRNA, CDS and gene boundaries from genbank annotation > files (e.g., "hs_chr19.gbs" from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/). > I've just switched from the biojava 1.22 to latest 1.3 release > (biojava-1.30-jdk14.jar and bytecode-0.92.jar) > and I get lots of exception (see below, the peace of code generating this follows as > well). Don't known if it's important but ".gbs" files do not hold the contig > sequences but only annotations. > > Nota: I am using the jdk 1.4.1. > > Thanks for your help. > > Charles Girardot > > ======================================= > java.lang.IllegalArgumentException: Location 59817 is outside 1..0 > at org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:306) > at > org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature.java:74) > at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source) > at > sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > at java.lang.reflect.Constructor.newInstance(Constructor.java:274) > at > org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138) > rethrown as org.biojava.bio.BioException: Couldn't realize feature > at > org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144) > at > org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94) > at > org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198) > at > org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204) > at > org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168) > at > org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87) > at > org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98) > at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) > at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34) > > > ========================================== > > package org.gc.test; > > import java.io.BufferedReader; > import java.io.File; > import java.io.FileReader; > > import org.biojava.bio.seq.Sequence; > import org.biojava.bio.seq.SequenceIterator; > import org.biojava.bio.seq.io.SeqIOTools; > > /** > * @author unknown > * > * To change the template for this generated type comment go to > * Window>Preferences>Java>Code Generation>Code and Comments > */ > public class GenbankParserTest { > > public static void main(String[] args) { > System.out.println("Main starts ..."); > try { > > File f = new File("D:\\Travail\\data\\Hs_chr19.gbs"); > BufferedReader bf = new BufferedReader(new FileReader(f)); > SequenceIterator it = SeqIOTools.readGenbank(bf); > while (it.hasNext()) { > System.out.println("getting next seq..."); > Sequence s = it.nextSequence(); > } > } catch (Exception e) { > System.out.println(e.getStackTrace()); > } > System.out.println("End of main"); > } > } > > ********** L'ADSL A 20 EUR/MOIS********** > Avec Tiscali, l'ADSL est � 20 EUR/mois. Vous pourrez chercher longtemps avant de > trouver moins cher ! > Pour profiter de cette offre exceptionnelle, cliquez ici : > http://register.tiscali.fr/adsl/ > Offre soumise � conditions. > > ------------------------------ > > Message: 4 > Date: Thu, 11 Sep 2003 09:40:34 +1200 > From: "Schreiber, Mark" <[EMAIL PROTECTED]> > Subject: RE: [Biojava-l] Reformating multiple sequence alignments > To: "Gabriel del Rio Guerra" <[EMAIL PROTECTED]>, > <[EMAIL PROTECTED]> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="UTF-8" > > Hi - > > I'm not too familiar with what you are trying to do but... > > A lot of the biojava Alignment API can be found in org.biojava.bio.alignment parsers > for reading and writing different formats are in org.biojava.bio.seq.io.* SeqIOTools > is especially useful. > > Hope this helps: > > - Mark > > > -----Original Message----- > From: Gabriel del Rio Guerra [mailto:[EMAIL PROTECTED] > Sent: Thu 11/09/2003 4:06 a.m. > To: [EMAIL PROTECTED] > Cc: > Subject: [Biojava-l] Reformating multiple sequence alignments > > > > Hi, > > I am interesting in using or developing a program to inter-convert > different sequence alignments formats. In particular I want to translate > HSSP alignments into MSF format. Does anyone knows if this is possible > with Biojava at this point? > > Thanks, > > Gabriel > > -----Original Message----- > From: Kenny Yu [mailto:[EMAIL PROTECTED] > Sent: Wednesday, April 30, 2003 8:45 AM > To: [EMAIL PROTECTED] > Subject: [Biojava-l] unified consolidated annotation system > > Both biosql and biodas are concerned with retrieving annotation on the > basis of known features. They are not optimized for large-scale > cross-system queries and data mining on the basis of annotations. I am > interested in consolidating annotations from various sources (such as > genbank and unigene) into a unified form on which I can run queries like > "find features that are linked to DNA repair function in human but not > in mouse" and "find feature whose molecular functions overlap with > those of Accession Number nnnn". Similar mechanisms may exist in LION's > SRS (http://www.lionbioscience.com/solutions/products/srs/relational). > What I am contemplating is essentially a data warehouse for annotations. > I'll borrow data warehouse and OLAP techniques in the design. It's a > hybrid of relational, nested-relational and multidimensional database. > Feature entity, or gene, and annotation are the dimensions. It models > textual values as well as binary objects such as pathway diagrams as > annot! > ation values. I intend to make my work open-source and would call it > UCAsql. Currently the schema design, with some documentation and java > API, is available to anyone upon request by email to myself at > [EMAIL PROTECTED] > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > ------------------------------ > > Message: 5 > Date: Thu, 11 Sep 2003 09:44:04 +1200 > From: "Schreiber, Mark" <[EMAIL PROTECTED]> > Subject: RE: [Biojava-l] Parsing location from gbk files > To: <[EMAIL PROTECTED]>, "biojava-l" > <[EMAIL PROTECTED]> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="UTF-8" > > Hi - > > This is a recurring problem as more files are being deposited that contain only > references to other contigs but contain annotation and features. > > A model where a DummySequence of appropriate length is instantiated if the contig > files are not available may be useful. Possibley a GBS parser would be useful? Has > anyone hacked out something like this? > > - Mark > > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > Sent: Thu 11/09/2003 6:13 a.m. > To: biojava-l > Cc: > Subject: [Biojava-l] Parsing location from gbk files > > > > Hi, > > I am using biojava to extract mRNA, CDS and gene boundaries from genbank > annotation files (e.g., "hs_chr19.gbs" from > ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/). > I've just switched from the biojava 1.22 to latest 1.3 release > (biojava-1.30-jdk14.jar and bytecode-0.92.jar) > and I get lots of exception (see below, the peace of code generating this > follows as well). Don't known if it's important but ".gbs" files do not hold the > contig sequences but only annotations. > > Nota: I am using the jdk 1.4.1. > > Thanks for your help. > > Charles Girardot > > > ======================================= > java.lang.IllegalArgumentException: Location 59817 is outside 1..0 > at > org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:306) > at > org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature.java:74) > at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown > Source) > at > sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > at java.lang.reflect.Constructor.newInstance(Constructor.java:274) > at > org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138) > rethrown as org.biojava.bio.BioException: Couldn't realize feature > at > org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144) > at > org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94) > at > org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198) > at > org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204) > at > org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168) > at > org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87) > at > org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98) > at > org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) > at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34) > > > > ========================================== > > package org.gc.test; > > import java.io.BufferedReader; > import java.io.File; > import java.io.FileReader; > > import org.biojava.bio.seq.Sequence; > import org.biojava.bio.seq.SequenceIterator; > import org.biojava.bio.seq.io.SeqIOTools; > > /** > * @author unknown > * > * To change the template for this generated type comment go to > * Window>Preferences>Java>Code Generation>Code and Comments > */ > public class GenbankParserTest { > > public static void main(String[] args) { > System.out.println("Main starts ..."); > try { > > File f = new File("D:\\Travail\\data\\Hs_chr19.gbs"); > BufferedReader bf = new BufferedReader(new FileReader(f)); > SequenceIterator it = SeqIOTools.readGenbank(bf); > while (it.hasNext()) { > System.out.println("getting next seq..."); > Sequence s = it.nextSequence(); > } > } catch (Exception e) { > System.out.println(e.getStackTrace()); > } > System.out.println("End of main"); > } > } > > > ********** L'ADSL A 20 EUR/MOIS********** > Avec Tiscali, l'ADSL est � 20 EUR/mois. Vous pourrez chercher longtemps > avant de trouver moins cher ! > Pour profiter de cette offre exceptionnelle, cliquez ici : > http://register.tiscali.fr/adsl/ > Offre soumise � conditions. > > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > ------------------------------ > > Message: 6 > Date: Thu, 11 Sep 2003 10:58:16 +0100 > From: Matthew Pocock <[EMAIL PROTECTED]> > Subject: Re: [Biojava-l] Parsing location from gbk files > To: "Schreiber, Mark" <[EMAIL PROTECTED]> > Cc: biojava-l <[EMAIL PROTECTED]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Schreiber, Mark wrote: > > >Hi - > > > >This is a recurring problem as more files are being deposited that contain only > >references to other contigs but contain annotation and features. > > > >A model where a DummySequence of appropriate length is instantiated if the contig > >files are not available may be useful. Possibley a GBS parser would be useful? Has > >anyone hacked out something like this? > > > >- Mark > > > > > It should be possible to create a dummy sequence of the right length and > then populate the feature table with component features for the assembly > info. Perhaps if we wrote a ComponentFeature that held an LSID - then > tries to resolve itself on demand via the LSID framework? > > I don't have the time right now, but somebody should get keen. > > Matthew > > > -----Original Message----- > > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > > Sent: Thu 11/09/2003 6:13 a.m. > > To: biojava-l > > Cc: > > Subject: [Biojava-l] Parsing location from gbk files > > > > > > > > Hi, > > > > I am using biojava to extract mRNA, CDS and gene boundaries from genbank > > annotation files (e.g., "hs_chr19.gbs" from > > ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/). > > I've just switched from the biojava 1.22 to latest 1.3 release > > (biojava-1.30-jdk14.jar and bytecode-0.92.jar) > > and I get lots of exception (see below, the peace of code generating this > > follows as well). Don't known if it's important but ".gbs" files do not hold the > > contig sequences but only annotations. > > > > Nota: I am using the jdk 1.4.1. > > > > Thanks for your help. > > > > Charles Girardot > > > > > > ======================================= > > java.lang.IllegalArgumentException: Location 59817 is outside 1..0 > > at > > org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:306) > > at > > org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature.java:74) > > at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown > > Source) > > at > > sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > > at java.lang.reflect.Constructor.newInstance(Constructor.java:274) > > at > > org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138) > > rethrown as org.biojava.bio.BioException: Couldn't realize feature > > at > > org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:144) > > at > > org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94) > > at > > org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:198) > > at > > org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:204) > > at > > org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:168) > > at > > org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:87) > > at > > org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98) > > at > > org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) > > at org.gc.test.GenbankParserTest.main(GenbankParserTest.java:34) > > > > > > > > ========================================== > > > > package org.gc.test; > > > > import java.io.BufferedReader; > > import java.io.File; > > import java.io.FileReader; > > > > import org.biojava.bio.seq.Sequence; > > import org.biojava.bio.seq.SequenceIterator; > > import org.biojava.bio.seq.io.SeqIOTools; > > > > /** > > * @author unknown > > * > > * To change the template for this generated type comment go to > > * Window>Preferences>Java>Code Generation>Code and Comments > > */ > > public class GenbankParserTest { > > > > public static void main(String[] args) { > > System.out.println("Main starts ..."); > > try { > > > > File f = new File("D:\\Travail\\data\\Hs_chr19.gbs"); > > BufferedReader bf = new BufferedReader(new FileReader(f)); > > SequenceIterator it = SeqIOTools.readGenbank(bf); > > while (it.hasNext()) { > > System.out.println("getting next seq..."); > > Sequence s = it.nextSequence(); > > } > > } catch (Exception e) { > > System.out.println(e.getStackTrace()); > > } > > System.out.println("End of main"); > > } > > } > > > > > > ********** L'ADSL A 20 EUR/MOIS********** > > Avec Tiscali, l'ADSL est � 20 EUR/mois. Vous pourrez chercher longtemps > > avant de trouver moins cher ! > > Pour profiter de cette offre exceptionnelle, cliquez ici : > > http://register.tiscali.fr/adsl/ > > Offre soumise � conditions. > > > > > > > > _______________________________________________ > > Biojava-l mailing list - [EMAIL PROTECTED] > > http://biojava.org/mailman/listinfo/biojava-l > > > > > > > >======================================================================= > >Attention: The information contained in this message and/or attachments > >from AgResearch Limited is intended only for the persons or entities > >to which it is addressed and may contain confidential and/or privileged > >material. Any review, retransmission, dissemination or other use of, or > >taking of any action in reliance upon, this information by persons or > >entities other than the intended recipients is prohibited by AgResearch > >Limited. If you have received this message in error, please notify the > >sender immediately. > >======================================================================= > > > >_______________________________________________ > >Biojava-l mailing list - [EMAIL PROTECTED] > >http://biojava.org/mailman/listinfo/biojava-l > > > > > > > > ------------------------------ > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > > End of Biojava-l Digest, Vol 9, Issue 2 > *************************************** ________________________________________________________________________ This e-mail has been scanned for all viruses by Star Internet. The service is powered by MessageLabs. 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