October 2004 Archives by thread

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Starting: Fri Oct 1 06:08:13 EST 2004
Ending: Sun Oct 31 06:36:28 EST 2004
Messages: 268

• [Bioperl-l] argument checking   Richard Adams
  • [Bioperl-l] argument checking   Aaron J. Mackey
• [Bioperl-l] Installation under Mac OS X   Andrew McArdle
  • [Bioperl-l] Installation under Mac OS X   Koen van der Drift
• [Bioperl-l] Ask help for Bio::Tools::Run::Primer3   Jason Stajich
  • [Bioperl-l] Ask help for Bio::Tools::Run::Primer3   Brian Osborne
    • [Bioperl-l] Ask help for Bio::Tools::Run::Primer3   Jason Stajich
• [Bioperl-l] Re: Bioperl-l Digest, Vol 18, Issue 1   Scott Cain
  • [Bioperl-l] typed sequence features   Allen Day
    • [Bioperl-l] Re: typed sequence features   Scott Cain
• [Bioperl-l] argument checking   Nathan (Nat) Goodman
• [Bioperl-l] argument checking   Aaron J. Mackey
  • [Bioperl-l] argument checking   Nathan (Nat) Goodman
• [Bioperl-l] Ask help for Bio::Tools::Run::Primer3   Fengkai Zhang (Tony)
• [Bioperl-l] Ask help for Bio::Tools::Run::Primer3   Fengkai Zhang (Tony)
• [Bioperl-l] Attention: upcoming BioPerl 1.5 developer's release   Jason Stajich
• [Bioperl-l] Questions on Representing Protein Ambiguity   Aaron J. Mackey
  • [Bioperl-l] Questions on Representing Protein Ambiguity   James Thompson
    • [Bioperl-l] Bioperl core 1.4 make error: line too long   Derek Gatherer
      • [Bioperl-l] Bioperl core 1.4 make error: line too long   Mike Schuh
      • [Bioperl-l] Bioperl core 1.4 make error: line too long   Jason Stajich
      • [Bioperl-l] Bioperl core 1.4 make error: line too long   Derek Gatherer
• [Bioperl-l] bioperl-run on Mac OS X   Koen van der Drift
• [Bioperl-l] How to volunteer for bioperl project?   Xiangli Zhang
  • [Bioperl-l] How to volunteer for bioperl project?   Aaron J. Mackey
• [Bioperl-l] Re:Installation under Mac OSX   Todd Naumann
  • [Bioperl-l] Re:Installation under Mac OSX   Jason Stajich
• [Bioperl-l] Will Spooner, where are you?   Aaron J. Mackey
  • [Bioperl-l] Will Spooner, where are you?   Will Spooner
• [Bioperl-l] pdb files/structure system   Douglas Kojetin
• [Bioperl-l] Attention: upcoming BioPerl 1.5 developer's release   James Thompson
  • [Bioperl-l] Attention: upcoming BioPerl 1.5 developer's release   Aaron J. Mackey
    • [Bioperl-l] Attention: upcoming BioPerl 1.5 developer's release   James Thompson
    • [Bioperl-l] Attention: upcoming BioPerl 1.5 developer's release   Brian Osborne
• [Bioperl-l] Bioperl core 1.4 make error: line too long   Jason Stajich
  • [Bioperl-l] Bioperl core 1.4 make error: line too long   Nathan Haigh
• [Bioperl-l] Phylogenetic tree   Li, Guoya
  • [Bioperl-l] Phylogenetic tree   Allen Day
• [Bioperl-l] t/RestrictionIO.t failing on perl 5.6.0   Jason Stajich
• [Bioperl-l] Bl2seq (cannot find path)   Marques Bonet
• [Bioperl-l] RE: Question: How do I run SwissPfam within Bioperl ?   Brian Osborne
  • [Bioperl-l] RE: Question: How do I run SwissPfam within Bioperl ?   Jason Stajich
• [Bioperl-l] Path to bl2seq   Marques Bonet
  • [Bioperl-l] Path to bl2seq   James Wasmuth
• [Bioperl-l] question about running lagan   Xiangli Zhang
• [Bioperl-l] Bio::Biblio question   Brian Osborne
• [Bioperl-l] Bio::Tools::Run::RemoteBlast hits limit   Jack Chen
• [Bioperl-l] Problems running BLAST Tutorial   Ranasaria, Kamal Kishor
• [Bioperl-l] GFF3 - Bioperl - SO   Steffen Grossmann
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Allen Day
  • [Bioperl-l] GFF3 - Bioperl - SO   Aaron J. Mackey
• [Bioperl-l] Path to bl2seq   Marques Bonet
• [Bioperl-l] Error with swissprot flat file parsing   Siddhartha Basu
• [Bioperl-l] Translation Question   Raymond Auerbach
• [Bioperl-l] Re: Integrating caBIOperl with BIOperl   Ewan Birney
• [Bioperl-l] Re:Path to bl2seq   Tomas Marques
• [Bioperl-l] From PDB to get nucleotide sequences for all related genomes?   "최상철"
  • [Bioperl-l] From PDB to get nucleotide sequences for all related genomes?   Jason Stajich
• [Bioperl-l] From PDB to get nucleotide sequences for all related genomes?   "최상철"
• [Bioperl-l] patch for Bio::SeqFeature::Tools::IDHandler.pm   Steffen Grossmann
  • [Bioperl-l] patch for Bio::SeqFeature::Tools::IDHandler.pm   Aaron J. Mackey
• [Bioperl-l] questions about run StandAloneBlast?   Sun, Jian
  • [Bioperl-l] questions about run StandAloneBlast?   Brian Osborne
• [Bioperl-l] acceptable PDB/structure formats   Douglas Kojetin
  • [Bioperl-l] acceptable PDB/structure formats   Jurgen Pletinckx
  • [Bioperl-l] acceptable PDB/structure formats   Brian Osborne
    • [Bioperl-l] acceptable PDB/structure formats   Douglas Kojetin
      • [Bioperl-l] acceptable PDB/structure formats   Gary
      • [Bioperl-l] acceptable PDB/structure formats   Douglas Kojetin
• [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Allen Day
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Steffen Grossmann
• [Bioperl-l] questions about run StandAloneBlast?   Sun, Jian
• [Bioperl-l] BLOSUM Matrix parser   zayed albertyn
  • [Bioperl-l] BLOSUM Matrix parser   Jason Stajich
• [Bioperl-l] questions about run StandAloneBlast?   Marc Logghe
• [Bioperl-l] basic problems with bioperl-db/biosql   Mikko Arvas
  • [Bioperl-l] basic problems with bioperl-db/biosql   Hilmar Lapp
    • [Bioperl-l] basic problems with bioperl-db/biosql   Mikko Arvas
      • [Bioperl-l] basic problems with bioperl-db/biosql   Hilmar Lapp
• [Bioperl-l] RE: problem solved !- questions about run StandAloneBlast?   Sun, Jian
• [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Allen Day
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Aaron J. Mackey
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Hilmar Lapp
    • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Allen Day
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Steffen Grossmann
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Steffen Grossmann
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Steffen Grossmann
• [Bioperl-l] problem with swissprot parsin   Siddhartha Basu
  • [Bioperl-l] problem with swissprot parsin   Brian Osborne
    • [Bioperl-l] problem with swissprot parsin   Siddhartha Basu
• [Bioperl-l] make test!!   Aaron J. Mackey
  • [Bioperl-l] make test!!   James Thompson
  • [Bioperl-l] make test!!   Brian Osborne
  • [Bioperl-l] make test!!   Hilmar Lapp
  • [Bioperl-l] make test!!   Nathan Haigh
  • [Bioperl-l] make test!!   Nathan Haigh
  • [Bioperl-l] make test!!   Nathan Haigh
  • [Bioperl-l] make test!!   Nathan Haigh
    • [Bioperl-l] make test!!   Brian Osborne
      • [Bioperl-l] make test!!   Nathan Haigh
      • [Bioperl-l] make test!!   Nathan Haigh
      • [Bioperl-l] make test!!   Nathan Spencer Haigh
    • [Bioperl-l] make test!!   Brian Osborne
      • [Bioperl-l] make test!!   Nathan Haigh
• [Bioperl-l] problem with swissprot parsin   Siddhartha Basu
  • [Bioperl-l] problem with swissprot parsin   Brian Osborne
    • [Bioperl-l] problem with swissprot parsin   Siddhartha Basu
      • [Bioperl-l] problem with swissprot parsin   Brian Osborne
      • [Bioperl-l] problem with swissprot parsin   Siddhartha Basu
      • [Bioperl-l] problem with swissprot parsin   Hilmar Lapp
      • [Bioperl-l] problem with swissprot parsin   Siddhartha Basu
      • [Bioperl-l] problem with swissprot parsin   Brian Osborne
      • [Bioperl-l] problem with swissprot parsin   Hilmar Lapp
      • [Bioperl-l] problem with swissprot parsin   Siddhartha Basu
      • [Bioperl-l] problem with swissprot parsin   Hilmar Lapp
• [Bioperl-l] counting gaps in sequence data   Michael Robeson
  • [Bioperl-l] counting gaps in sequence data   Michael Cipriano
  • [Bioperl-l] counting gaps in sequence data   Barry Moore
    • [Bioperl-l] counting gaps in sequence data   Michael S. Robeson II
      • [Bioperl-l] counting gaps in sequence data   Barry Moore
• [Bioperl-l] parsing SwissProt records -- need help   Anand Venkatraman
• [Bioperl-l] problem parsing SwissProt Records   Anand Venkatraman
• [Bioperl-l] problems with the Bio::Tools::Run::Genewise module   Jack Chen
• [Bioperl-l] It seems a bug: Bio/SeqFeatureI.pm?   Sang Chul Choi
  • [Bioperl-l] It seems a bug: Bio/SeqFeatureI.pm?   Hilmar Lapp
• [Bioperl-l] problems with the Bio::Tools::Run::Genewise module   Jack Chen
• [Bioperl-l] data structure returned from tribeMCL   Michael Bradley
• [Bioperl-l] Deprecating   Brian Osborne
  • [Bioperl-l] Deprecating   Allen Day
  • [Bioperl-l] Deprecating   Stefan Kirov
    • [Bioperl-l] Deprecating   Brian Osborne
      • [Bioperl-l] Deprecating   Stefan Kirov
      • [Bioperl-l] Deprecating   Brian Osborne
      • [Bioperl-l] Deprecating   Stefan Kirov
      • [Bioperl-l] Deprecating   Brian Osborne
      • [Bioperl-l] Deprecating   Stefan Kirov
  • [Bioperl-l] Deprecating   Steve Chervitz
• [Bioperl-l] Deprecating   Brian Osborne
• [Bioperl-l] Counting gaps in sequence data revisited.   Michael S. Robeson II
• [Bioperl-l] nmake - windows   Nathan Haigh
• [Bioperl-l] Re: Counting gaps in sequence data revisited.   Michael S. Robeson II
• [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Allen Day
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Steffen Grossmann
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Hilmar Lapp
    • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Allen Day
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Steffen Grossmann
  • [Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO   Steffen Grossmann
• [Bioperl-l] Aligning BLAST results   Andrew McArdle
• [Bioperl-l] Bio::Tools::Glimmer   michael watson (IAH-C)
• [Bioperl-l] RandomSeqIO   Jean-Marc Frigerio
• [Bioperl-l] Bio::SearchIO TFASTX parsing bug   Daniel Mascarenhas
  • [Bioperl-l] Bio::SearchIO TFASTX parsing bug   Aaron J. Mackey
• [Bioperl-l] problems with bioperl's Bio::SeqIO::qual   Carlos Mauricio La Rota
  • [Bioperl-l] problems with bioperl's Bio::SeqIO::qual   Brian Osborne
• [Bioperl-l] friendlier bioperl-guts-l messages   Allen Day
• [Bioperl-l] Re: Installing BioPerl under Mac OS X   Madeleine Lemieux
  • [Bioperl-l] RE: Installing BioPerl under Mac OS X   Andrew McArdle
  • [Bioperl-l] Re: Installing BioPerl under Mac OS X   Koen van der Drift
    • [Bioperl-l] Re: Installing BioPerl under Mac OS X   Sean Davis
      • [Bioperl-l] Re: Installing BioPerl under Mac OS X   Koen van der Drift
    • [Bioperl-l] Re: Installing BioPerl under Mac OS X   Madeleine Lemieux
      • [Bioperl-l] Re: Installing BioPerl under Mac OS X   Koen van der Drift
      • [Bioperl-l] Re: Installing BioPerl under Mac OS X   Sean Davis
      • [Bioperl-l] Re: Installing BioPerl under Mac OS X   Koen van der Drift
• [Bioperl-l] Test Message   Nathan Haigh
  • [Bioperl-l] Test Message   Steffen Grossmann
• [Bioperl-l] Another test - form my ne defaults   Nathan Haigh
• [Bioperl-l] Another test - form my new defaults   Nathan Haigh
• [Bioperl-l] Another test - form my new defaults   Nathan Haigh
• [Bioperl-l] Another test - form my new defaults   Nathan Haigh
• [Bioperl-l] Another test - form my new defaults   Nathan Haigh
• [Bioperl-l] last test!   Nathan Haigh
• [Bioperl-l] last test   Nathan Haigh
• [Bioperl-l] last test 3   Nathan Haigh
• [Bioperl-l] last test 4   Nathan Haigh
• [Bioperl-l] last test 5   Nathan Haigh
• [Bioperl-l] last test 6   Nathan Haigh
• [Bioperl-l] creating a simplealign object from strings   luisa pugliese
  • [Bioperl-l] creating a simplealign object from strings   Remo Sanges
  • [Bioperl-l] creating a simplealign object from strings   Nathan Haigh
• [Bioperl-l] make test failures   Aaron J. Mackey
• [Bioperl-l] Handling gff3 Target and Dbxref tags through FeatureIO   Scott Cain
  • [Bioperl-l] Re: Handling gff3 Target and Dbxref tags through FeatureIO   Allen Day
    • [Bioperl-l] Re: Handling gff3 Target and Dbxref tags through FeatureIO   Scott Cain
      • [Bioperl-l] Re: Handling gff3 Target and Dbxref tags through FeatureIO   Scott Cain
      • [Bioperl-l] Re: Handling gff3 Target and Dbxref tags through FeatureIO   Allen Day
      • [Bioperl-l] Re: Handling gff3 Target and Dbxref tags through FeatureIO   Scott Cain
      • [Bioperl-l] Re: Handling gff3 Target and Dbxref tags through FeatureIO   Hilmar Lapp
• [Bioperl-l] Problems installing Bio::DB   Sudha S
  • [Bioperl-l] Problems installing Bio::DB   Hilmar Lapp
    • [Bioperl-l] Problems installing Bio::DB   Brian Osborne
    • [Bioperl-l] Problems installing Bio::DB   Chris Fields
• [Bioperl-l] V`icodin, free shipping   Tammie Gabriel
• [Bioperl-l] EMBL Identifier line is incorrect when using SeqIO (1.4)   michael watson (IAH-C)
  • [Bioperl-l] EMBL Identifier line is incorrect when using SeqIO (1.4)   Hilmar Lapp
    • [Bioperl-l] EMBL Identifier line is incorrect when using SeqIO (1.4)   Bernhard Schmalhofer
• [Bioperl-l] extracting sequences by id from simplealign object   luisa pugliese
• [Bioperl-l] reading an alignment   luisa pugliese
• [Bioperl-l] How to check if a file exists in a large directory   ted Huang
• [Bioperl-l] Bio::DB::GFF getting a spliced sequence   Morten Lindow
• [Bioperl-l] make test!!   Brian Osborne
  • [Bioperl-l] make test!!   Nathan Haigh
    • [Bioperl-l] make test!!   Brian Osborne
      • [Bioperl-l] make test!!   Nathan Haigh
• [Bioperl-l] make test!!   Brian Osborne
• [Bioperl-l] make test!!   Brian Osborne
• [Bioperl-l] problems with Bio::Graph::ProteinGraph   Maria Persico
• [Bioperl-l] EMBL Identifier line is incorrect when using SeqIO(1.4)   simon andrews (BI)
• [Bioperl-l] EMBL Identifier line is incorrect when using SeqIO (1.4)   michael watson (IAH-C)
• [Bioperl-l] Bioblio_biofetch.t failure on windows   Nathan Haigh
• [Bioperl-l] Glyph Bump bug   Gabriele Bucci
• [Bioperl-l] make test!!   Brian Osborne
• FW: [Bioperl-l] make test!!   Brian Osborne
  • [Bioperl-l] make test!!   Nathan Haigh
    • [Bioperl-l] make test!!   Brian Osborne
    • [Bioperl-l] make test!!   Brian Osborne
• [Bioperl-l] make test!!   Nathan Haigh
  • [Bioperl-l] make test!!   Nathan Haigh
• [Bioperl-l] comparing data between hashes   Michael S. Robeson II
  • [Bioperl-l] comparing data between hashes   Brian Osborne
    • [Bioperl-l] comparing data between hashes   Michael Robeson
    • [Bioperl-l] comparing data between hashes   Michael S. Robeson II
• [Bioperl-l] make test!!   Nathan Haigh
  • [Bioperl-l] make test!!   Brian Osborne
• [Bioperl-l] Bio::Tools::SimpleAnalysisBase triggers Data::Dumper core dump on FreeBSD 4   Peter van Heusden
• [Bioperl-l] Bug in Bio::FeatureIO::gff   Steffen Grossmann
• [Bioperl-l] Fwd: How to check if a file exists in a large directory   ted Huang
• [Bioperl-l] bioperl problem   Ying Sun
  • [Bioperl-l] bioperl problem   Brian Osborne
• [Bioperl-l] Re: Bioperl-DB question   Hilmar Lapp
• [Bioperl-l] Bio::Index::Fasta difficulty   Guojun Yang
  • [Bioperl-l] Bio::Index::Fasta difficulty   Brian Osborne
    • [Bioperl-l] Bio::Index::Fasta difficulty   Guojun Yang
• [Bioperl-l] update to Bio::Tools::Run::EMBOSSacd   smontgom at bcgsc.ca
• [Bioperl-l] total_combos addition for Bio::Tools::IUPAC   smontgom at bcgsc.ca
• [Bioperl-l] Having problems with parsing SwissProt Records   Anand Venkatraman
  • [Bioperl-l] Having problems with parsing SwissProt Records   Hilmar Lapp
    • [Bioperl-l] Reply to Hilmar Lapp's solution -- parsing SwissProt Records   Anand Venkatraman
      • [Bioperl-l] Reply to Hilmar Lapp's solution -- parsing SwissProt Records   Jason Stajich
• [Bioperl-l] SCF file get_header call   Sam Kalat
• [Bioperl-l] failing tests on OS X   Jason Stajich
• [Bioperl-l] Reply to Hilmar Lapp's solution -- parsing SwissProt Records   Jason Stajich
  • [Bioperl-l] Obtaining GO cross-references from SwissProt Records --reply to Jason Stajich's solution   Anand Venkatraman
• [Bioperl-l] Bioperl 1.4 - Can't locate object method "start" via package "Bio::Seq::RichSeq"   michael watson (IAH-C)
• [Bioperl-l] Parsing Blast reports: Length of sequence of a hit ?   Edith Schlagenhauf
  • [Bioperl-l] Parsing Blast reports: Length of sequence of a hit ?   Jason Stajich
• [Bioperl-l] (no subject)   Chris Fields
• [Bioperl-l] Problems installing Bio::DB   Chris Fields
• [Bioperl-l] Reconstructing BLAST output   Adam Woolfe
  • [Bioperl-l] Reconstructing BLAST output   Jason Stajich
    • [Bioperl-l] Reconstructing BLAST output   Will Spooner
• [Bioperl-l] SCF get_header stopped working   samkalat at sneakrets.com
• [Bioperl-l] making msf file from the array of sequence string   Kwangbom Choi
  • [Bioperl-l] making msf file from the array of sequence string   Nathan Haigh
  • [Bioperl-l] TCoffee   Kwangbom Choi
• [Bioperl-l] help on pdb   ani
  • [Bioperl-l] help on pdb   Ed Green
• [Bioperl-l] how to create Graphics object from home-made SQL table with parsed blast data?   Marcus Claesson
  • [Bioperl-l] how to create Graphics object from home-made SQL table with parsed blast data?   Jan Aerts
  • [Bioperl-l] how to create Graphics object from home-made SQL table with parsed blast data?   Sean Davis
• [Bioperl-l] load_ontology.pl crashes   Mikko Arvas
  • [Bioperl-l] load_ontology.pl crashes   Hilmar Lapp
• [Bioperl-l] Cont: load_ontology.pl crashes   Mikko Arvas
  • [Bioperl-l] Cont: load_ontology.pl crashes   Hilmar Lapp
• [Bioperl-l] help on pdb   ani
• [Bioperl-l] nmake test   Nathan Haigh

Last message date: Sun Oct 31 06:36:28 EST 2004
Archived on: Sun Oct 31 06:35:04 EST 2004

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