March 2006 Archives by thread

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Starting: Wed Mar 1 02:41:08 UTC 2006
Ending: Sat Apr 1 04:26:53 UTC 2006
Messages: 246

• [Bioperl-l] WGS sequences through Bio::DB::GenBank   Chris Fields
• [Bioperl-l] pSW question- hanging tails of alignments   Jon Manning
  • [Bioperl-l] pSW question- hanging tails of alignments   Jason Stajich
• [Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"   Harald
  • [Bioperl-l] newbie tries StandAloneBlast and receives "cant openBLOSUM62"   Chris Fields
  • [Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"   Torsten Seemann
    • [Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"   Chris Fields
      • [Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"   Harald
      • [Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"   Chris Fields
      • [Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"   Harald
      • [Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"   Chris Fields
• [Bioperl-l] Problem with bp_pg_bulk_load_gff   Scott Cain
  • [Bioperl-l] Problem with bp_pg_bulk_load_gff   Marco Blanchette
• [Bioperl-l] WGS sequences through Bio::DB::GenBank   Chris Fields
  • [Bioperl-l] WGS sequences through Bio::DB::GenBank   Chris Fields
• [Bioperl-l] (no subject)   Praveen Raj
  • [Bioperl-l] (no subject)   Jason Stajich
• [Bioperl-l] Bio::Tools::Run::* extending   Rutger Vos
  • [Bioperl-l] Bio::Tools::Run::* extending   Chris Fields
  • [Bioperl-l] Bio::Tools::Run::* extending   Brian Osborne
• [Bioperl-l] SeqHound User Support   Unleashed Informatics Administration
• [Bioperl-l] Unleashed Informatics Supports DogBox Online Community   Unleashed Informatics Administration
  • [Bioperl-l] Unleashed Informatics Supports DogBox Online Community   Chris Fields
• [Bioperl-l] SeqHound User Support   Unleashed Informatics Administration
• [Bioperl-l] Substitution models   Rutger Vos
  • [Bioperl-l] Substitution models   Jason Stajich
• [Bioperl-l] How to print a generic matrix?   Sam Al-Droubi
• [Bioperl-l] Feature extraction using Bio::DB::GFF   Marco Blanchette
• [Bioperl-l] How to print a generic matrix?   Sam Al-Droubi
• [Bioperl-l] Feature extraction using Bio::DB::GFF   Marc Logghe
• [Bioperl-l] How to print a generic matrix?   Jordan Mark Swanson
• [Bioperl-l] bioperl API conventions   Rutger Vos
  • [Bioperl-l] bioperl API conventions   Chris Fields
  • [Bioperl-l] bioperl API conventions   Hilmar Lapp
• [Bioperl-l] seq_word and pattern counts   Torsten Seemann
• [Bioperl-l] Bio::DB::BioDB - insert failed. Dupllicate entry '' for key 2?   Jay Hannah
  • [Bioperl-l] Bio::DB::BioDB - insert failed. Dupllicate entry '' for key 2?   Chris Fields
    • [Bioperl-l] Bio::DB::BioDB - insert failed. Dupllicate entry '' for key 2?   Jay Hannah
      • [Bioperl-l] Bio::DB::BioDB - insert failed. Dupllicate entry '' for key 2?   Chris Fields
  • [Bioperl-l] Bio::DB::BioDB - insert failed. Dupllicate entry '' for key 2?   Hilmar Lapp
• [Bioperl-l] Bio::DB::BioDB - insert failed. Dupllicate entry ''for key 2?   Marc Logghe
• [Bioperl-l] Bio::DB::BioDB - insert failed. Dupllicate entry ''for key 2?   Marc Logghe
• [Bioperl-l] Suggestion about Bio::Structure::SecStr::DSSP::Res   Zhiqiang Ye
  • [Bioperl-l] Suggestion about Bio::Structure::SecStr::DSSP::Res   Brian Osborne
  • [Bioperl-l] Suggestion about Bio::Structure::SecStr::DSSP::Res   Torsten Seemann
    • [Bioperl-l] Suggestion about Bio::Structure::SecStr::DSSP::Res   Zhiqiang Ye
• [Bioperl-l] bptutorial.pl won't run   Philip M Terry
  • [Bioperl-l] bptutorial.pl won't run   Brian Osborne
  • [Bioperl-l] bptutorial.pl won't run   Sam Al-Droubi
• [Bioperl-l] <no subject>   Marco Blanchette
  • [Bioperl-l] <no subject>   Lincoln Stein
  • [Bioperl-l] <no subject>   Lincoln Stein
  • [Bioperl-l] <no subject>   Lincoln Stein
    • [Bioperl-l] Bio::DB::GFF and GadFly GFF3 issues   Marco Blanchette
      • [Bioperl-l] Bio::DB::GFF and GadFly GFF3 issues   Lincoln Stein
    • [Bioperl-l] small mistake found in documentation of bioperl-1.5.0-RC1   Harald
      • [Bioperl-l] small mistake found in documentation of bioperl-1.5.0-RC1   Brian Osborne
• [Bioperl-l] NCBI's seq_gene.md file   Ryan Golhar
  • [Bioperl-l] NCBI's seq_gene.md file   Brian Osborne
    • [Bioperl-l] NCBI's seq_gene.md file   Sean Davis
  • [Bioperl-l] NCBI's seq_gene.md file   Cui, Wenwu (NIH/NCI) [F]
• [Bioperl-l] contigs in NCBIHelper (RE: WGS sequences through Bio::DB::GenBank)   Chris Fields
• [Bioperl-l] Bio::TreeIO functions   Lucia Peixoto
  • [Bioperl-l] Bio::TreeIO functions   Jason Stajich
    • [Bioperl-l] Bio::TreeIO functions   Lucia Peixoto
      • [Bioperl-l] Bio::TreeIO functions   Jason Stajich
      • [Bioperl-l] Bio::TreeIO functions   Georgii A Bazykin
      • [Bioperl-l] Bio::TreeIO functions   Jason Stajich
• [Bioperl-l] Which interfaces to use for phylogenetics?   Rutger Vos
  • [Bioperl-l] Which interfaces to use for phylogenetics?   Brian Osborne
• [Bioperl-l] Bio::TreeIO parse from a string?   Rutger Vos
  • [Bioperl-l] Bio::TreeIO parse from a string?   Hilmar Lapp
• [Bioperl-l] WGS file problems with Bio::SeqIO::genbank   Chris Fields
• [Bioperl-l] New Microbial Bioinformatics Resource Center open   Chris Larsen
  • [Bioperl-l] New Microbial Bioinformatics Resource Center open   Chris Fields
• [Bioperl-l] ncDNA   Chris Fields
  • [Bioperl-l] ncDNA   Chris Fields
• [Bioperl-l] codontree   amit p bafana
• [Bioperl-l] EMBL/genbank organism parsing   James Abbott
  • [Bioperl-l] EMBL/genbank organism parsing   Hilmar Lapp
  • [Bioperl-l] EMBL/genbank organism parsing   Jason Stajich
• [Bioperl-l] not getting all exons back when using Bio::DB::GFF   Niels Klitgord
  • [Bioperl-l] not getting all exons back when using Bio::DB::GFF   Lincoln Stein
• [Bioperl-l] seq_word and pattern counts   Staffa, Nick (NIH/NIEHS) [C]
• [Bioperl-l] WGS, WGS_SCAFLD support added for GenBank files   Chris Fields
  • [Bioperl-l] WGS, WGS_SCAFLD support added for GenBank files   Brian Osborne
    • [Bioperl-l] WGS, WGS_SCAFLD support added for GenBank files   Chris Fields
      • [Bioperl-l] WGS, WGS_SCAFLD support added for GenBank files   Brian Osborne
      • [Bioperl-l] WGS, WGS_SCAFLD support added for GenBank files   Chris Fields
• [Bioperl-l] Initial benchmarking of Bio::DB::GFF3   Lincoln Stein
• [Bioperl-l] help on blastcl3   Sanjib Kumar Gupta
  • [Bioperl-l] help on blastcl3   Chris Fields
• [Bioperl-l] decoding strand of hit in e-PCR output using Bio::Tools::EPCR   Cook, Malcolm
• [Bioperl-l] where to document dependency? AND new SeqIO formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene   Cook, Malcolm
  • [Bioperl-l] where to document dependency? AND new SeqIO formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene   Brian Osborne
    • [Bioperl-l] where to document dependency? AND new SeqIO formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene   Chris Fields
• [Bioperl-l] parsing blast results : how to get the length of the proteinseq   Hubert Prielinger
  • [Bioperl-l] parsing blast results : how to get the length of the proteinseq   Jason Stajich
• [Bioperl-l] where to document dependency? AND new SeqIO formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene   Cook, Malcolm
  • [Bioperl-l] where to document dependency? AND new SeqIO formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene   Chris Fields
• [Bioperl-l] Multiple gene segment problem   Marco Blanchette
  • [Bioperl-l] Multiple gene segment problem   Lincoln Stein
• [Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast   neeti somaiya
  • [Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast   Chris Fields
    • [Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast   Rutger Vos
    • [Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast   Torsten Seemann
      • [Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast   Chris Fields
      • [Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast   neeti somaiya
      • [Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast   Chris Fields
      • [Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast   neeti somaiya
      • [Bioperl-l] urgent help required - syntax for usingparamatersdifferent from default in standalone blast   Chris Fields
      • [Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast   neeti somaiya
• [Bioperl-l] _READMETHOD default   Brian Osborne
  • [Bioperl-l] _READMETHOD default   Torsten Seemann
  • [Bioperl-l] _READMETHOD default   Jason Stajich
• [Bioperl-l] translating a GenBank file   Derek Gatherer
• [Bioperl-l] genbank2gff3.pl on new human RefSeq   Ed Green
• [Bioperl-l] EMBL/genbank organism parsing   James Abbott
• [Bioperl-l] Finding all human paralogues   Yuval Itan
  • [Bioperl-l] Finding all human paralogues   Torsten Seemann
    • [Bioperl-l] Finding all human paralogues   Yuval Itan
    • [Bioperl-l] Finding all human paralogues   Yuval Itan
      • [Bioperl-l] Finding all human paralogues   Torsten Seemann
      • [Bioperl-l] Finding all human paralogues   Yuval Itan
      • [Bioperl-l] Finding all human paralogues   Torsten Seemann
      • [Bioperl-l] Finding all human paralogues   Yuval Itan
• [Bioperl-l] update to bp_remote_blast.pl   Evan
  • [Bioperl-l] update to bp_remote_blast.pl   Brian Osborne
• [Bioperl-l] Parsing entrezgene with Bio::SeqIO   Liisa Koski
  • [Bioperl-l] Parsing entrezgene with Bio::SeqIO   Mingyi Liu
  • [Bioperl-l] Parsing entrezgene with Bio::SeqIO   Stefan Kirov
    • [Bioperl-l] Parsing entrezgene with Bio::SeqIO   Liisa Koski
      • [Bioperl-l] Parsing entrezgene with Bio::SeqIO   Stefan Kirov
  • [Bioperl-l] Parsing entrezgene with Bio::SeqIO   Stefan Kirov
• [Bioperl-l] can't locate object method "next_result" (probably a simple problem)   Andrew Norman
  • [Bioperl-l] can't locate object method "next_result" (probably a simple problem)   Harald
  • [Bioperl-l] can't locate object method "next_result" (probably a simple problem)   Torsten Seemann
    • [Bioperl-l] can't locate object method "next_result" (probably a simple problem)   Shawn Hoon
      • [Bioperl-l] can't locate object method "next_result" (probablya simple problem)   Chris Fields
  • [Bioperl-l] can't locate object method "next_result" (probably a simple problem)   Brian Osborne
    • [Bioperl-l] can't locate object method "next_result" (probably a simple problem)   Chris Fields
• [Bioperl-l] Correlation coefficient?   Sam Al-Droubi
• [Bioperl-l] Correlation coefficient?   Sam Al-Droubi
  • [Bioperl-l] Correlation coefficient?   Jason Stajich
• [Bioperl-l] Correlation coefficient?   Cui, Wenwu (NIH/NCI) [F]
  • [Bioperl-l] Correlation coefficient?   Sam Al-Droubi
• [Bioperl-l] Sporadic Failure to retrieve Sequence Objects from GenPept   Warren Gallin
  • [Bioperl-l] Sporadic Failure to retrieve Sequence Objects from GenPept   Torsten Seemann
• [Bioperl-l] Hi! everyone   r93626012 at ntu.edu.tw
  • [Bioperl-l] Hi! everyone   Chris Fields
    • [Bioperl-l] Hi! everyone   Chris Fields
• [Bioperl-l] how to "tile" the HSPs of a hit-object ?   Harald
  • [Bioperl-l] how to "tile" the HSPs of a hit-object ?   Steve_Chervitz
    • [Bioperl-l] how to "tile" the HSPs of a hit-object ?   Harald
      • [Bioperl-l] how to "tile" the HSPs of a hit-object ?   Steve_Chervitz
• [Bioperl-l] where to document dependency? AND new SeqIO formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene   Cook, Malcolm
  • [Bioperl-l] where to document dependency? AND new SeqIO formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene   Chris Dagdigian
• [Bioperl-l] Missing methods in SearchUtils and GenericHit   Steve_Chervitz
• [Bioperl-l] Hi! everyone   Chris Fields
• [Bioperl-l] Bio::Registry & Bio::DB::Flat   Mike Muratet
  • [Bioperl-l] Bio::Registry & Bio::DB::Flat   khoueiry
    • [Bioperl-l] Bio::Registry & Bio::DB::Flat   Mike Muratet
• [Bioperl-l] Bio::Registry & Bio::DB::Flat   Mike Muratet
• [Bioperl-l] Request for comments: Bio::DB::GFF3 namespace   Lincoln Stein
  • [Bioperl-l] Request for comments: Bio::DB::GFF3 namespace   Hilmar Lapp
  • [Bioperl-l] Request for comments: Bio::DB::GFF3 namespace   Torsten Seemann
• [Bioperl-l] Random access to subsequences using OBDA or bio::db::flat   Sean Davis
• [Bioperl-l] convert xyz coordinates to distance   ni_psis
  • [Bioperl-l] convert xyz coordinates to distance   Boris Steipe
• [Bioperl-l] cannot find path to wublast   Jyoti Shah
  • [Bioperl-l] cannot find path to wublast   Torsten Seemann
    • [Bioperl-l] cannot find path to wublast   Jyoti Shah
    • [Bioperl-l] cannot find path to wublast   Jyoti Shah
• [Bioperl-l] question about revision 1.17 of Bio::Index::AbstractSeq.pm   Scott Markel
  • [Bioperl-l] question about revision 1.17 of Bio::Index::AbstractSeq.pm   Brian Osborne
  • [Bioperl-l] question about revision 1.17 of Bio::Index::AbstractSeq.pm   Chris Fields
    • [Bioperl-l] question about revision 1.17 of Bio::Index::AbstractSeq.pm   Scott Markel
• [Bioperl-l] Thursday   Roger Hall
• [Bioperl-l] error   sonmitra mondal
  • [Bioperl-l] error   Chris Fields
• [Bioperl-l] Quantum computing   Roger Hall
  • [Bioperl-l] Quantum computing   Chris Fields
• [Bioperl-l] genbank species parsing (genbank.pm,v 1.121)   David Waner
• [Bioperl-l] Species name validation problem   David Waner
  • [Bioperl-l] Species name validation problem   Hilmar Lapp
• [Bioperl-l] Important news for developers on open-bio machines   Chris Dagdigian
• [Bioperl-l] MeSH term retrieval   Michael Seewald
  • [Bioperl-l] MeSH term retrieval   Hilmar Lapp
    • [Bioperl-l] MeSH term retrieval   Michael Seewald
      • [Bioperl-l] MeSH term retrieval   t-nakazato at muj.biglobe.ne.jp
  • [Bioperl-l] MeSH term retrieval   Brian Osborne
    • [Bioperl-l] MeSH term retrieval   Michael Seewald
• [Bioperl-l] bptutorial.pl question, and appropriate bioperl version question   Philip M Terry
  • [Bioperl-l] bptutorial.pl question, and appropriate bioperl version question   Sam Al-Droubi
  • [Bioperl-l] bptutorial.pl question, and appropriate bioperl version question   Chris Fields
• [Bioperl-l] help needed   Alex Stanley
• [Bioperl-l] clustalw.exe   Katrin
  • [Bioperl-l] clustalw.exe   Katrin
    • [Bioperl-l] clustalw.exe   Chris Fields
• [Bioperl-l] Species name validation problem   David Waner
  • [Bioperl-l] Species name validation problem   Hilmar Lapp
• [Bioperl-l] error   Chris Fields
• [Bioperl-l] Announcing BOSC 2006   Darin London
• [Bioperl-l] error   Chris Fields
• [Bioperl-l] Question: How to manipulate files   Michael Craige
  • [Bioperl-l] Question: How to manipulate files   Marco Blanchette
  • [Bioperl-l] Question: How to manipulate files   Brian Osborne
• [Bioperl-l] Bio::DB::GFF3 nightmare   Marco Blanchette
  • [Bioperl-l] Bio::DB::GFF3 nightmare   Lincoln Stein
  • [Bioperl-l] Bio::DB::GFF3 nightmare   Lincoln Stein
• [Bioperl-l] Bio::DB::GFF still a nightmare...   Marco Blanchette
  • [Bioperl-l] Bio::DB::GFF still a nightmare...   Lincoln Stein
    • [Bioperl-l] Bio::DB::GFF still a nightmare...   Marco Blanchette
• [Bioperl-l] TraceSearch   Adam Spargo
  • [Bioperl-l] [Genome] TraceSearch   Jim Kent
• [Bioperl-l] Error: The extension 'Bio::SeqIO::staden::read' is not properly installed in path   CJay Horton
  • [Bioperl-l] Error: The extension 'Bio::SeqIO::staden::read' is not properly installed in path   Brian Osborne
• [Bioperl-l] What happens to STDOUT?   Ryan Golhar
  • [Bioperl-l] What happens to STDOUT?   Torsten Seemann
    • [Bioperl-l] What happens to STDOUT?   Chris Fields
• [Bioperl-l] possible bug printing GenBank feature qualfiers   Scott Markel
  • [Bioperl-l] possible bug printing GenBank feature qualfiers   Chris Fields
    • [Bioperl-l] possible bug printing GenBank feature qualfiers   Scott Markel
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Chris Fields
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Hilmar Lapp
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Scott Markel
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Chris Fields
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Chris Fields
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Hilmar Lapp
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Chris Fields
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Scott Markel
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Brian Osborne
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Hilmar Lapp
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Chris Fields
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Chris Fields
      • [Bioperl-l] possible bug printing GenBank feature qualfiers   Torsten Seemann
• [Bioperl-l] What happens to STDOUT?   Marc Logghe
  • [Bioperl-l] What happens to STDOUT?   Roy Chaudhuri
    • [Bioperl-l] What happens to STDOUT?   Ryan Golhar
• [Bioperl-l] Issue with Bio::SearchIO::psl (was: Bioperl bug 1977)   Chris Fields
• [Bioperl-l] What happens to STDOUT?   Marc Logghe
• [Bioperl-l] What happens to STDOUT?   Marc Logghe
• [Bioperl-l] Batch mode in Bio::DB::GenBank   Marc Logghe
  • [Bioperl-l] Batch mode in Bio::DB::GenBank   Chris Fields
    • [Bioperl-l] Batch mode in Bio::DB::GenBank   Hilmar Lapp
• [Bioperl-l] possible bug printing GenBank feature qualfiers   Chris Fields

Last message date: Sat Apr 1 04:26:53 UTC 2006
Archived on: Mon Jun 16 02:46:46 UTC 2014

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