November 2004 Archives by thread

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Starting: Mon Nov 1 03:19:11 EST 2004
Ending: Tue Nov 30 16:22:18 EST 2004
Messages: 257

• [Bioperl-l] Adapt source method in Bio::SeqFeature::Annotated   Steffen Grossmann
  • [Bioperl-l] Adapt source method in Bio::SeqFeature::Annotated   Allen Day
    • [Bioperl-l] Adapt source method in Bio::SeqFeature::Annotated   Steffen Grossmann
• [Bioperl-l] nmake test   Nathan Haigh
  • [Bioperl-l] BioPerl CVS EOL Inconsistency   Nathan Haigh
    • [Bioperl-l] BioPerl CVS EOL Inconsistency   Nathan Haigh
      • [Bioperl-l] BioPerl CVS EOL Inconsistency   Brian Osborne
• [Bioperl-l] Problems installing Bio::DB   Sudha S
• Re [Bioperl-l] Parsing Blast reports: GI number of a hit ?   Edith Schlagenhauf
  • Re [Bioperl-l] Parsing Blast reports: GI number of a hit ?   Jason Stajich
    • Re [Bioperl-l] Parsing Blast reports: GI number of a hit ?   Malay
    • [Bioperl-l] getting proteins matching GO   Pedro Antonio Reche
      • [Bioperl-l] getting proteins matching GO   Stefan Kirov
      • [Bioperl-l] getting proteins matching GO   Pedro Antonio Reche
      • [Bioperl-l] getting proteins matching GO   Stefan Kirov
• [Bioperl-l] about Bio::Annotation::Collection   Scott Cain
  • [Bioperl-l] about Bio::Annotation::Collection   Steffen Grossmann
    • [Bioperl-l] about Bio::Annotation::Collection   Allen Day
      • [Bioperl-l] about Bio::Annotation::Collection   Jason Stajich
• [Bioperl-l] update to Bio::Tools::Run::EMBOSSacd   Brian Osborne
• [Bioperl-l] BioPerl on Linux....   Peter G Carswell
• [Bioperl-l] BioPerl on Linux....   James Thompson
• [Bioperl-l] Bioperl help needed!   Zara Ghazoui
  • [Bioperl-l] Bioperl help needed!   Jason Stajich
• [Bioperl-l] How do I bl2seq remotely?   Uri David Akavia
• [Bioperl-l] Bioperl help needed!   Zara Ghazoui
  • [Bioperl-l] Bioperl help needed!   Jason Stajich
• [Bioperl-l] Bioperl help needed!   Jason Stajich
• [Bioperl-l] A mechanism to store quality values for sequences in a BioSQL-db   Carlos Mauricio La Rota
• [Bioperl-l] RE: Integrating caBIOperl with BIOperl   Covitz, Peter (NIH/NCI)
  • [Bioperl-l] RE: Integrating caBIOperl with BIOperl   Lincoln Stein
• [Bioperl-l] mis-match position in HSP   Sucheta Tripathy
  • [Bioperl-l] mis-match position in HSP   Jason Stajich
• [Bioperl-l] Problems with "tblastx"-like output and GFF   Neil Saunders
• [Bioperl-l] CGI Perl and Bioperl   hafiz hafiz
• [Bioperl-l] graphing trees   Guillaume Rousse
  • [Bioperl-l] graphing trees   Jason Stajich
    • [Bioperl-l] graphing trees   Guillaume Rousse
• [Bioperl-l] RE: Integrating caBIOperl with BIOperl   Covitz, Peter (NIH/NCI)
  • [Bioperl-l] RE: Integrating caBIOperl with BIOperl   Hilmar Lapp
    • [Bioperl-l] RE: Integrating caBIOperl with BIOperl   Steve Chervitz Trutane
      • [Bioperl-l] RE: Integrating caBIOperl with BIOperl   Steve Chervitz
• [Bioperl-l] graphing trees   Guillaume Rousse
  • [Bioperl-l] graphing trees   Sean Davis
    • [Bioperl-l] graphing trees   Brian O'Connor
• [Bioperl-l] Blast Results IO to Local RDBMS   Barry Moore
• [Bioperl-l] how to insert more than one features?   hafiz hafiz
• [Bioperl-l] Length of ID in EMBL sequence entries   Daniel Lang
• [Bioperl-l] problem using 'add_sub_SeqFeature' on home-made blast parsed data in mysql table   Marcus Claesson
• [Bioperl-l] Length of ID in EMBL sequence entries   simon andrews (BI)
  • [Bioperl-l] Length of ID in EMBL sequence entries   Daniel Lang
• [Bioperl-l] comparing phylogenies.   Zara Ghazoui
  • [Bioperl-l] comparing phylogenies.   Jason Stajich
• [Bioperl-l] RE: Integrating caBIOperl with BIOperl   Covitz, Peter (NIH/NCI)
• [Bioperl-l] remote blast   Karolina Zavisek
• [Bioperl-l] Bio::DB::Query::GenBank   Ligia Mateiu
  • [Bioperl-l] Bio::DB::Query::GenBank   Wuming Gong
    • [Bioperl-l] Bio::DB::Query::GenBank   Aaron J. Mackey
• [Bioperl-l] Bioperl methods and classes diagram ?   S.P.T.Krishnan
• [Bioperl-l] Length of ID in EMBL sequence entries   Daniel Lang
• [Bioperl-l] Length of ID in EMBL sequence entries   simon andrews (BI)
• [Bioperl-l] Calculating distances from PDB files   Robinson, Peter
• [Bioperl-l] local blast   Nathan Haigh
• [Bioperl-l] graphing trees   Guillaume Rousse
  • [Bioperl-l] graphing trees   Sean Davis
• [Bioperl-l] Problems installing GD   Barry Moore
  • [Bioperl-l] Problems installing GD   Dave Howorth
    • [Bioperl-l] Problems installing GD   Lincoln Stein
    • [Bioperl-l] Problems installing GD   Barry Moore
      • [Bioperl-l] Problems installing GD   Lincoln Stein
  • [Bioperl-l] Problems installing GD   Lincoln Stein
• [Bioperl-l] RE: Problems installing GD Solved.   Andy Hammer
• [Bioperl-l] Error using Bio::DB::SwissProt   Susan J. Miller
  • [Bioperl-l] Error using Bio::DB::SwissProt   Hilmar Lapp
• [Bioperl-l] getting proteins matching GO   Davis, Sean (NIH/NHGRI)
  • [Bioperl-l] getting proteins matching GO   Stefan A Kirov
• [Bioperl-l] getting proteins matching GO   Nathan (Nat) Goodman
  • [Bioperl-l] getting proteins matching GO   Pedro Antonio Reche
    • [Bioperl-l] getting proteins matching GO   Nathan (Nat) Goodman
      • [Bioperl-l] Remote Blast error - 500 Too many open files   Affan Qureshi
• [Bioperl-l] Re: Error using Bio::DB::SwissProt   Anand Venkatraman
• [Bioperl-l] RemoteBlast: No Significant Matches (works for web interface)   affan qureshi
• [Bioperl-l] Patched (Bugfix) Releases   Mark Johnson
  • [Bioperl-l] Patched (Bugfix) Releases   Aaron J. Mackey
• [Bioperl-l] RemoteBlast: No Significant Matches (works for web interface)   Affan Qureshi
  • [Bioperl-l] RemoteBlast: No Significant Matches (works for web interface)   Jason Stajich
• [Bioperl-l] MEME parsing   Sean Davis
  • [Bioperl-l] MEME parsing   Sean Davis
  • [Bioperl-l] MEME parsing   Stefan Kirov
• [Bioperl-l] dynamically making a matrix   Michael Robeson
• [Bioperl-l] BioPerl installation for SGI   Waibhav Tembe
• [Bioperl-l] Fix for Bio::Tools::Blat   Neil Saunders
  • [Bioperl-l] Fix for Bio::Tools::Blat   Brian Osborne
• [Bioperl-l] getting proteins matching GO   Chris Mungall
• [Bioperl-l] 1.5.0-RC1 available for download   Aaron J. Mackey
  • [Bioperl-l] Re: 1.5.0-RC1 available for download   Aaron J. Mackey
  • [Bioperl-l] Re: 1.5.0-RC1 available for download   Aaron J. Mackey
    • [Bioperl-l] Re: 1.5.0-RC1 available for download   Brian Osborne
      • [Bioperl-l] Re: 1.5.0-RC1 available for download   Nathan Haigh
      • [Bioperl-l] Re: 1.5.0-RC1 available for download   Aaron J. Mackey
      • [Bioperl-l] Re: 1.5.0-RC1 available for download   Hilmar Lapp
      • [Bioperl-l] Re: 1.5.0-RC1 available for download   Jason Stajich
      • [Bioperl-l] Re: 1.5.0-RC1 available for download   amackey at pcbi.upenn.edu
      • [Bioperl-l] Re: 1.5.0-RC1 available for download   Allen Day
      • [Bioperl-l] Re: 1.5.0-RC1 available for download   Hilmar Lapp
• [Bioperl-l] BioSeq method errors with BioSQL sequences   Barry Moore
• [Bioperl-l] BioSeq method errors with BioSQL sequences   Marc Logghe
  • [Bioperl-l] BioSeq method errors with BioSQL sequences   Hilmar Lapp
• [Bioperl-l] RemoteBlast with same e-val (10 vs 1e-10) works   Madeleine Lemieux
• [Bioperl-l] SeqIO File locking   Dave Thompson
  • [Bioperl-l] SeqIO File locking   James Thompson
  • [Bioperl-l] SeqIO File locking   Jason Stajich
• [Bioperl-l] gap position script   Michael S. Robeson II
• [Bioperl-l] gap position script   Michael Robeson
• [Bioperl-l] TIGR parser for SeqIO   Ed Robinson
  • [Bioperl-l] TIGR parser for SeqIO   Josh Lauricha
  • [Bioperl-l] TIGR parser for SeqIO   Josh Lauricha
• [Bioperl-l] getting proteins matching GO   Ian Donaldson
• [Bioperl-l] remote blast put HITLIST_SIZE = 1000   Madeleine Lemieux
• [Bioperl-l] remote blast DESCRIPTIONS   Madeleine Lemieux
• [Bioperl-l] problem installing bioperl-ext   Alicia Amadoz
  • [Bioperl-l] problem installing bioperl-ext   Guillaume Rousse
  • [Bioperl-l] problem installing bioperl-ext   Barry Moore
• [Bioperl-l] (no subject)   Ying Sun
• [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm, 1.16, 1.17   Allen Day
  • [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm, 1.16, 1.17   Steffen Grossmann
    • [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm, 1.16, 1.17   Chris Mungall
      • [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm, 1.16, 1.17   Lincoln Stein
      • [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm, 1.16, 1.17   Allen Day
• [Bioperl-l] Divide and Assemble   michael watson (IAH-C)
• [Bioperl-l] Subseq that transfers features too   michael watson (IAH-C)
  • [Bioperl-l] Subseq that transfers features too   Jason Stajich
• [Bioperl-l] Kazusa Codon Table DB : Bio::DB::DBCUTG   Peter van Heusden
  • [Bioperl-l] Kazusa Codon Table DB : Bio::DB::DBCUTG   Mitsuteru NAKAO
• [Bioperl-l] bioperl-1.4 make error   Shengsheng Zhang
  • [Bioperl-l] bioperl-1.4 make error   Jason Stajich
• [Bioperl-l] Bio::SeqIO and bad entries in uniprot and interpro   Mikko Arvas
  • [Bioperl-l] Bio::SeqIO and bad entries in uniprot and interpro   Jason Stajich
    • [Bioperl-l] Bio::SeqIO and bad entries in uniprot and interpro   Hilmar Lapp
      • [Bioperl-l] Bio::SeqIO and bad entries in uniprot and interpro   Mikko Arvas
    • [Bioperl-l] Bio::SeqIO and bad entries in uniprot and interpro   Mikko Arvas
• [Bioperl-l] Bio::Tools::Genewise.pm problems   michael watson (IAH-C)
  • [Bioperl-l] Bio::Tools::Genewise.pm problems   Jason Stajich
• [Bioperl-l] Bio::Tools::Genewise.pm problems   michael watson (IAH-C)
• [Bioperl-l] make test errors   Allen Day
  • [Bioperl-l] make test errors   Jason Stajich
    • [Bioperl-l] make test errors   Jason Stajich
      • [Bioperl-l] make test errors   amackey at pcbi.upenn.edu
    • [Bioperl-l] Module for finding consensus   Edward WIJAYA
• [Bioperl-l] SeqFeature::Annotated broken   Scott Cain
  • [Bioperl-l] Re: SeqFeature::Annotated broken   Allen Day
• [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Allen Day
  • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Hilmar Lapp
    • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Jason Stajich
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Aaron J. Mackey
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Allen Day
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Aaron J. Mackey
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Allen Day
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Chris Mungall
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Jason Stajich
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Allen Day
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Jason Stajich
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Chris Mungall
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Allen Day
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Jason Stajich
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Allen Day
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Chris Mungall
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Allen Day
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Hilmar Lapp
      • XML vs AnnotationCollectionI [was Re: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes]   Chris Mungall
      • XML vs AnnotationCollectionI [was Re: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes]   Aaron J. Mackey
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Aaron J. Mackey
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Hilmar Lapp
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Hilmar Lapp
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Aaron J. Mackey
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Hilmar Lapp
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Aaron J. Mackey
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Steffen Grossmann
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Allen Day
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Allen Day
      • [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes   Chris Mungall
• [Bioperl-l] Point me in the right direction--chromosomal positions   Tomso, Dan (NIH/NIEHS)
  • [Bioperl-l] Point me in the right direction--chromosomal positions   Sean Davis
• [Bioperl-l] How to setup a local database of genbank?   ted Huang
• [Bioperl-l] Blast return codes (fwd)   Matthew Laird
• [Bioperl-l] Re: [Bioperl-guts-l] SeqFeature::Annotated->add_SeqFeature with 'EXPAND' option.   Allen Day
• [Bioperl-l] bad entries in interpro   Robson Francisco de Souza {S}
  • [Bioperl-l] bad entries in interpro   Allen Day
  • [Bioperl-l] bad entries in interpro   Allen Day
    • [Bioperl-l] bad entries in interpro   Hilmar Lapp
    • [Bioperl-l] bad entries in interpro   Hilmar Lapp
      • [Bioperl-l] bad entries in interpro   Allen Day
  • [Bioperl-l] bad entries in interpro   Hilmar Lapp
• [Bioperl-l] Easy switching from wwwBlast to QBlast   Madeleine Lemieux
  • [Bioperl-l] Easy switching from wwwBlast to QBlast   Jason Stajich
• [Bioperl-l] More on bioperl-live/Bio/FeatureIO gff.pm   Steffen Grossmann
• [Bioperl-l] question on abi module   Ramiro Barrantes
• [Bioperl-l] How can I get add_sub_SeqFeature to work as I want?   Marcus Claesson
  • [Bioperl-l] How can I get add_sub_SeqFeature to work as I want?   Allen Day
    • [Bioperl-l] How can I get add_sub_SeqFeature to work as I want?   Aaron J. Mackey
    • [Bioperl-l] How can I get add_sub_SeqFeature to work as I want?   Jason Stajich
• [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.16, 1.17   Allen Day
  • [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.16, 1.17   Steffen Grossmann
  • [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.16, 1.17   Hilmar Lapp
    • [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.16, 1.17   Allen Day
• [Bioperl-l] Core dump in t/protgraph on FreeBSD   Peter van Heusden
  • [Bioperl-l] Core dump in t/protgraph on FreeBSD   Fernan Aguero
    • [Bioperl-l] Core dump in t/protgraph on FreeBSD   Aaron J. Mackey
      • [Bioperl-l] Core dump in t/protgraph on FreeBSD   Peter van Heusden
      • [Bioperl-l] Core dump in t/protgraph on FreeBSD   Peter van Heusden
      • [Bioperl-l] Core dump in t/protgraph on FreeBSD   Fernan Aguero
• [Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.17, 1.18   Allen Day
  • [Bioperl-l] Annotated.pm   Hilmar Lapp
    • [Bioperl-l] Annotated.pm   Allen Day
      • [Bioperl-l] Annotated.pm   Hilmar Lapp
      • [Bioperl-l] Annotated.pm   Hilmar Lapp
      • [Bioperl-l] Annotated.pm   Allen Day
      • [Bioperl-l] Annotated.pm   Hilmar Lapp
      • [Bioperl-l] Annotated.pm   Hilmar Lapp
      • tags and annotations, was Re: [Bioperl-l] Annotated.pm   Steffen Grossmann
      • [Bioperl-l] Annotated.pm   Aaron J. Mackey
      • [Bioperl-l] Annotated.pm   Allen Day
• [Bioperl-l] getting teh NO HITS FOUND with SearchIO   Javier Terol
  • [Bioperl-l] getting teh NO HITS FOUND with SearchIO   Edith Schlagenhauf
  • [Bioperl-l] getting teh NO HITS FOUND with SearchIO   Barry Moore
• [Bioperl-l] more questins about SearchIO   Javier Terol
  • [Bioperl-l] more questins about SearchIO   Jason Stajich
• [Bioperl-l] Parsing Hit/Query Frames from Blastx   davila
  • [Bioperl-l] Parsing Hit/Query Frames from Blastx   Jason Stajich
• [Bioperl-l] bl2seq   Karolina Zavisek
  • [Bioperl-l] bl2seq   Brian Osborne
• [Bioperl-l] print out species from swiss prot?   hafiz hafiz
  • [Bioperl-l] print out species from swiss prot?   Jason Stajich
• [Bioperl-l] Help with BioGraphics   davila
• [Bioperl-l] Bio::DB::Query::GenBank   Marc Logghe
  • [Bioperl-l] Bio::DB::Query::GenBank   Jason Stajich
• [Bioperl-l] LWP.pm   Soojin Yi
  • [Bioperl-l] LWP.pm   James Thompson
  • [Bioperl-l] LWP.pm   Barry Moore
• [Bioperl-l] Re: Bioperl   Barry Moore
• [Bioperl-l] Bio::DB::Query::GenBank   Marc Logghe
• [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   Mike Cariaso
  • [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   Ian Korf
    • [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   Malay
      • [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   Ian Korf
      • [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   Steve Chervitz
      • [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   Michael Maibaum
      • [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   Jason Stajich
    • [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   Tim Cutts
      • [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   Ian Korf
      • [Bioperl-l] Re: [Bioclusters] BioPerl and memory handling   James Cuff
• [Bioperl-l] SearchIO and bl2seq blast reports   Bill Kenworthy
  • [Bioperl-l] SearchIO and bl2seq blast reports   Jason Stajich
    • [Bioperl-l] SearchIO and bl2seq blast reports   Bill Kenworthy
• [Bioperl-l] SearchIO broken   Brian Osborne
• [Bioperl-l] Re: [Bioclusters] BioPerl 1.2.3 and memory handling   Jason Stajich

Last message date: Tue Nov 30 16:22:18 EST 2004
Archived on: Tue Nov 30 16:54:20 EST 2004

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