From mark.schreiber at group.novartis.com Sun Aug 1 21:00:43 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Sun Aug 1 21:02:11 2004 Subject: [Biojava-l] got identity? Message-ID: >From memory most of this stuff goes into the Annotation objects of the objects and features that the parser creates. Take each object and dump it's Annotation to SYSOUT and you'll soon find out where everything ends up. Hongyu Zhang Sent by: biojava-l-bounces@portal.open-bio.org 08/01/2004 01:13 AM To: Hongyu Zhang cc: biojava-l@biojava.org Subject: [Biojava-l] got identity? Is there any method to get the percentage of identities of BLAST hsps in Biojava? Once again, I followed the guide in the "Biojava in anger". Its code successfully parsed a WU-BLAST result, and printed out the hit E-value and ID nicely, but when I tried to look for the method to return HSP identities, I had no luck. It's such a common feature of BLAST result, so it caught me quite off-guard. Thanks! --Hongyu _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From Russell.Smithies at agresearch.co.nz Mon Aug 2 00:17:49 2004 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon Aug 2 00:19:16 2004 Subject: [Biojava-l] Sun Developer Newsletter demonstrates NCBI SOAP Message-ID: The latest "SDN Enterprise Java Technology Tech Tips" newsletter has some good stuff on accessing NCBI's webservices with SOAP and transforming the resulting XML with an XSLT TransformerFactory(). You can view it online at the address below. http://java.sun.com/developer/EJTechTips/2004/tt0730.html Russell Smithies Bioinformatics Software Developer AgResearch Invermay Mosgiel New Zealand ======================================================================= 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. ======================================================================= From fardpa at mail.nih.gov Fri Aug 6 11:36:48 2004 From: fardpa at mail.nih.gov (Fard, Payam (NIH/NCI)) Date: Fri Aug 6 11:38:07 2004 Subject: [Biojava-l] SeqIOTools.readSwissprot API Message-ID: <16A0583FB1644E4DB8C0A0265028B6FD811C08@nihexchange13.nih.gov> Hi all, I am using the following program to read a swissProt file, but I am getting "Could not read sequence exception". I am using jdk 1.4.2_04-b05 and bioJava 1.4pre1. Any ideas what I am doing wrong? import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; import java.io.*; import org.biojava.bio.*; import java.util.*; public class ReadSwiss { public static void main(String[] args) { BufferedReader br = null; try { //create a buffered reader to read the sequence file specified by args[0] br = new BufferedReader(new FileReader(args[0])); } catch (FileNotFoundException ex) { //can't find the file specified by args[0] ex.printStackTrace(); System.exit(-1); } //read the SwissProt File SequenceIterator sequences = SeqIOTools.readSwissprot(br); //iterate through the sequences while(sequences.hasNext()){ try { Sequence seq = sequences.nextSequence(); //do stuff with the sequence System.out.println("Sequence length is : " + seq.length()); System.out.println("Sequence name is : " + seq.getName()); } catch (BioException ex) { //not in SwissProt format ex.printStackTrace(); }catch (NoSuchElementException ex) { //request for more sequence when there isn't any ex.printStackTrace(); } } } } I am getting the following exception: [java] org.biojava.bio.BioException: Could not read sequence [java] at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader .java:104) [java] at ReadSwiss.main(ReadSwiss.java:30) [java] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [java] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcces sorImpl.java:39) [java] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMet hodAccessorImpl.java:25) [java] at java.lang.reflect.Method.invoke(Method.java:324) [java] at org.apache.tools.ant.taskdefs.ExecuteJava.run(ExecuteJava.jav a:208) [java] at org.apache.tools.ant.taskdefs.ExecuteJava.execute(ExecuteJava .java:150) [java] at org.apache.tools.ant.taskdefs.Java.run(Java.java:443) [java] at org.apache.tools.ant.taskdefs.Java.executeJava(Java.java:163) [java] at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108) [java] at org.apache.tools.ant.Task.perform(Task.java:341) [java] at org.apache.tools.ant.Target.execute(Target.java:309) [java] at org.apache.tools.ant.Target.performTasks(Target.java:336) [java] at org.apache.tools.ant.Project.executeTarget(Project.java:1339) [java] at org.apache.tools.ant.Project.executeTargets(Project.java:1255 ) [java] at org.apache.tools.ant.Main.runBuild(Main.java:609) [java] at org.apache.tools.ant.Main.start(Main.java:196) [java] at org.apache.tools.ant.Main.main(Main.java:235) [java] Caused by: java.io.IOException: Premature end of stream or missing e nd tag '//' for EMBL [java] at org.biojava.bio.seq.io.EmblLikeFormat.readSequence(EmblLikeFo rmat.java:267) [java] at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader .java:101) Thanks, Payam. From mmatilai at hytti.uku.fi Tue Aug 10 09:04:45 2004 From: mmatilai at hytti.uku.fi (mmatilai@hytti.uku.fi) Date: Tue Aug 10 09:05:50 2004 Subject: [Biojava-l] GenBank files and weight matrices Message-ID: <1092143085.4118c7ed4cbd5@maili.uku.fi> Hi, I'd like to search a GenBank file with a weight matrix. My idea was to create a simple weight matrix and then iterate through the file using a sequence iterator moving forward with the hasNext command. At each iteration the new sequence would then be annotated with the weightmatrix method annotate(seq) and the positions and scores of matches reported in a for loop. Apparently this is not as straight-forward since i get a match from beginning of the sequence file until end and a bioexception is declared before the score is reported. I found also the Cookbook recipe and tried the exact code from this just with the modification that i was using a genbank file with sequence iterator to get the sequences and i have the same problem. Should I do sth different to annotate the sequence in a GenBank file with my weight matrix? Is the sequence iterator the problem? How is it working actually, what part of the file does it read at one iteration? Best regards Merja From mmatilai at hytti.uku.fi Fri Aug 13 06:19:37 2004 From: mmatilai at hytti.uku.fi (mmatilai@hytti.uku.fi) Date: Fri Aug 13 06:20:45 2004 Subject: [Biojava-l] Sequence IO Message-ID: <1092392377.411c95b9114bd@maili.uku.fi> Hi, I'm writing a program that processes GenBank files and adds annotations. It would be desirable that these annotations are saved (to a GenBank file). There is a GenbankFileFormer class available but I couldn't figure it out how to use it. Has someone tried this? Merja From avinash238 at rediffmail.com Fri Aug 13 02:37:37 2004 From: avinash238 at rediffmail.com (katikaneni avinash rao) Date: Fri Aug 13 13:09:59 2004 Subject: [Biojava-l] multiple sequence alignments Message-ID: <20040813063737.26059.qmail@webmail27.rediffmail.com> hi, does anyone know how to implement Multiple sequence alignment algorithm in Java( preferabbly Biojava). If anyone knows it please send it urgently. Your help will be appriciated Avinash From mark.schreiber at group.novartis.com Fri Aug 13 14:26:21 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Fri Aug 13 14:27:21 2004 Subject: [Biojava-l] Update of BioJava In Anger-Japanese Message-ID: Hi all - The BioJava in Anger Japanese translation has kindly been updated by Kentaro and Takeshi. I am travelling for the next few weeks but I will update the link when I get home (unless Thomas or Matthew get there first). For now, follow the link below. Thanks again to Kentaro and Takeshi! - Mark ----- Forwarded by Mark Schreiber/GP/Novartis on 08/14/2004 02:22 AM ----- Takeshi Sasayama 08/13/2004 11:27 PM To: Mark Schreiber/GP/Novartis@PH cc: honshistu@yahoo.co.jp Subject: Update of BioJava In Anger-Japanese Hello Mark, Mr. Kentaro Sugino and I have updated "BioJava In Anger" Japanese translation pages. And now we have our website in Japan and please change the link to this URL. http://www.geocities.jp/bio_portal/bj_in_anger_ja/ Thank you Takeshi Sasayama From max_dipl at web.de Mon Aug 16 02:50:39 2004 From: max_dipl at web.de (Maximilian Haussler) Date: Mon Aug 16 02:52:42 2004 Subject: [Biojava-l] old webpage Message-ID: <4120593F.90606@web.de> Hi, I just want to mention this, although it's kind of obvious: the instructions given on http://cvs.biojava.org/ look pretty outdated... Max From willy_valdivia at orionbiosciences.com Tue Aug 17 03:10:09 2004 From: willy_valdivia at orionbiosciences.com (willy_valdivia@orionbiosciences.com) Date: Tue Aug 17 03:11:00 2004 Subject: [Biojava-l] Virtual Conference on Genomics and Bioinformatics Message-ID: <20040817071009.30937.qmail@webmail01.mesa1.secureserver.net> Fourth Virtual Conference on Genomics and Bioinformatics ********************************************************************************** September 21-24, 2004 Virtual Conference Sites Around the World ********************************************************************************** The Virtual Conference on Genomics and Bioinformatics is an advanced collaborative environment featuring high profile researchers involved in the development and use of cutting edge technologies and approaches which allow a better understanding of the molecular structure and dynamics of biological systems. No registration fees is required, however, the filling the registration form is required in order to participate. This information is used for the virtual conference ONLY and for the selection of discussion leaders and panel members. The registration ensures a seat reservation in the site nearest you. Participant registration page: http://www.virtualgenomics.org/conference_2004.htm Speakers and program: http://www.virtualgenomics.org/program_2004.htm Uri Alon, Weizmann Institute of Science. Israel Wanda Andreoni, IBM Zürich Research Laboratory, Switzerland Kim Baldridge, Universität Zürich. Switzerland Patsy Babbitt. University of California, San Francisco. USA Irene Bosch, University of Massachusetts Medical School. USA Carlos Camacho, University of Pittsburgh, USA Colin C. Collins, Medicine and Cancer Research Institute, UCSF. USA Charles DeLisi, Boston University. USA Frank Gibbons, Harvard University. USA Martin Gollery, University of Nevada at Reno. USA Fern Hunt, National Institute of Standards and Technology. USA S.S. Iyengar, Louisiana State University. USA Steven F. Jennings, University of Arkansa at Little Rock, USA Maricel Kann, National Institutes of Health. NCBI. USA Eugene Koonin, National Institutes of Health. USA Luis Rocha, Los Alamos National Laboratory. USA John B. Shabb, University of North Dakota. USA Wibke Sudholt, Universität Zürich. Switzerland Christoph W. Sensen, University of Calgary. Canada Richard Simon, National Institutes of Health. NCI. USA Jason Suen, California Institute of Technology, USA Sarah B. Tegen, National Academy of Sciences, USA William Perrizo, North Dakota State University. USA Willy Valdivia-Granda. Orion Integrated Biosciences. USA Yuzhen Ye, The Burnham Institute. USA Roie Yerushalmi, Weizmann Institute of Science. Israel Problems with your registration: e-mail registration@virtualgenomics.org Thank you Willy Valdivia-Granda Founder of the Virtual Conferences on Genomics and Bioinformatics From mark.schreiber at group.novartis.com Tue Aug 24 21:57:53 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Aug 24 21:58:32 2004 Subject: [Biojava-l] biojava presentation Message-ID: Hello all - I have made a few updates to the Biojava in Anger web page. Firstly I have added a link to a powerpoint presentation I have used a few times that describes the core API and some of the phylosophy behind it (~700KB download). I have also updated the link to the new japanese translation of BJIA. Finally I have made some modifications to the transcription and translation examples to reflect the change from RNATools.transcribe() to DNATools.toRNA() in BioJava 1.4 (soon to be released???) Let me know if anything doesn't work. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910