January 2007 Archives by thread

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Starting: Mon Jan 1 20:17:42 UTC 2007
Ending: Wed Jan 31 23:27:30 UTC 2007
Messages: 256

• [Bioperl-l] acquiring a local refseq + index   Erik
  • [Bioperl-l] acquiring a local refseq + index   Chris Fields
    • [Bioperl-l] acquiring a local refseq + index   Erik
      • [Bioperl-l] acquiring a local refseq + index   Chris Fields
• [Bioperl-l] repeatmasker   Karen Buysse
  • [Bioperl-l] repeatmasker   Mauricio Herrera Cuadra
    • [Bioperl-l] repeatmasker   Nathan S. Haigh
      • [Bioperl-l] repeatmasker   Karen Buysse
      • [Bioperl-l] repeatmasker   Chris Fields
  • [Bioperl-l] repeatmasker   Fairley, Derek
  • [Bioperl-l] repeatmasker   Sendu Bala
  • [Bioperl-l] repeatmasker   Nathan S. Haigh
  • [Bioperl-l] repeatmasker   Chris Fields
• [Bioperl-l] store variations, generate sequences   Marian Thieme
  • [Bioperl-l] store variations, generate sequences   Albert Vilella
• [Bioperl-l] quiet() proposed for WrapperBase   Sendu Bala
  • [Bioperl-l] quiet() proposed for WrapperBase   Chris Fields
• [Bioperl-l] store variations, generate sequences   Marian thieme
  • [Bioperl-l] store variations, generate sequences   Brian Osborne
• [Bioperl-l] PopGen   Albert Vilella
• [Bioperl-l] Assignment problem :(   Kurt Gobain
  • [Bioperl-l] Assignment problem :(   Sean Davis
    • [Bioperl-l] Assignment problem :(   Mauricio Herrera Cuadra
  • [Bioperl-l] Assignment problem :(   Florin Iucha
  • [Bioperl-l] Assignment problem :(   Kurt Gobain
• [Bioperl-l] Auto-method caller proposal   Sendu Bala
  • [Bioperl-l] Auto-method caller proposal   Chris Fields
    • [Bioperl-l] Auto-method caller proposal   Sendu Bala
      • [Bioperl-l] Auto-method caller proposal   Chris Fields
      • [Bioperl-l] Auto-method caller proposal   Sendu Bala
      • [Bioperl-l] Auto-method caller proposal   Chris Fields
  • [Bioperl-l] Auto-method caller proposal   aaron.j.mackey at gsk.com
    • [Bioperl-l] Auto-method caller proposal   Sendu Bala
  • [Bioperl-l] Auto-method caller proposal   Hilmar Lapp
    • [Bioperl-l] Auto-method caller proposal   Sendu Bala
      • [Bioperl-l] Auto-method caller proposal   Hilmar Lapp
      • [Bioperl-l] Auto-method caller proposal   Sendu Bala
      • [Bioperl-l] Auto-method caller proposal   Chris Fields
• [Bioperl-l] PopGen   Albert Vilella
• [Bioperl-l] Bio::Tools RNA modules   Chris Fields
• [Bioperl-l] Auto-method caller proposal   Rutger Vos
• [Bioperl-l] Mask vector   Staffa, Nick (NIH/NIEHS)
  • [Bioperl-l] Mask vector   Jason Stajich
• [Bioperl-l] (no subject)   Andrew Stewart
  • [Bioperl-l] (no subject)   Jason Stajich
    • [Bioperl-l] (no subject)   Andrew Stewart
      • [Bioperl-l] (no subject)   Chris Fields
      • [Bioperl-l] (no subject)   Sendu Bala
      • [Bioperl-l] Bioperl wiki 'working examples' - SeqIO HOWTO   Erik
      • [Bioperl-l] Bioperl wiki 'working examples' - SeqIO HOWTO   Brian Osborne
      • [Bioperl-l] Bioperl wiki 'working examples' - SeqIO HOWTO   Erik
• [Bioperl-l] Bioperl wiki 'working examples' - SeqIO HOWTO   Kevin Brown
• [Bioperl-l] Graphics Panel   Kevin Brown
  • [Bioperl-l] Graphics Panel   Torsten Seemann
• [Bioperl-l] Error while running load_seqdatabase.pl   George Heller
  • [Bioperl-l] Error while running load_seqdatabase.pl   Hilmar Lapp
• [Bioperl-l] Auto-method caller proposal   Nathan (Nat) Goodman
  • [Bioperl-l] Auto-method caller proposal   Sendu Bala
    • [Bioperl-l] Auto-method caller proposal   Nathan (Nat) Goodman
      • [Bioperl-l] Auto-method caller proposal   Sendu Bala
      • [Bioperl-l] Auto-method caller proposal   Nathan (Nat) Goodman
      • [Bioperl-l] Auto-method caller proposal   Sendu Bala
      • [Bioperl-l] Auto-method caller proposal   David Messina
      • [Bioperl-l] Auto-method caller proposal   Sendu Bala
      • [Bioperl-l] Auto-method caller proposal   Chris Fields
• [Bioperl-l] Error while running load_seqdatabase.pl   George Heller
• [Bioperl-l] Question on Tree : Last common ancestor / Internal Nodes   Himanshu Ardawatia
  • [Bioperl-l] Question on Tree : Last common ancestor / Internal Nodes   Sendu Bala
    • [Bioperl-l] Question on Tree : Last common ancestor / Internal Nodes   Himanshu Ardawatia
      • [Bioperl-l] Question on Tree : Last common ancestor / Internal Nodes   Jason Stajich
      • [Bioperl-l] Question on Tree : Last common ancestor / Internal Nodes   Sendu Bala
      • [Bioperl-l] Question on Tree : Last common ancestor / Internal Nodes   Chris Fields
      • [Bioperl-l] Question on Tree : Last common ancestor / Internal Nodes   Himanshu Ardawatia
• [Bioperl-l] problem with Bio::SearchIO::Writer   lidaof
  • [Bioperl-l] problem with Bio::SearchIO::Writer   David Messina
    • [Bioperl-l] problem with Bio::SearchIO::Writer   lidaof
      • [Bioperl-l] problem with Bio::SearchIO::Writer   David Messina
      • [Bioperl-l] problem with Bio::SearchIO::Writer   Chris Fields
      • [Bioperl-l] problem with Bio::SearchIO::Writer   lidaof
      • [Bioperl-l] problem with Bio::SearchIO::Writer   David Messina
      • [Bioperl-l] problem with Bio::SearchIO::Writer   lidaof
      • [Bioperl-l] problem with Bio::SearchIO::Writer   lidaof
• [Bioperl-l] Graphics Panel   Kevin Brown
  • [Bioperl-l] Graphics Panel   Lincoln Stein
• [Bioperl-l] Bio::PopGen::IO   Marian Thieme
  • [Bioperl-l] Bio::PopGen::IO   Jason Stajich
    • [Bioperl-l] Bio::PopGen::IO   Marian Thieme
      • [Bioperl-l] Bio::PopGen::IO   Jason Stajich
• [Bioperl-l] bp_seqfeature_load of latest Flybase GFF annotation fails due to data inconsistency.   Cook, Malcolm
• [Bioperl-l] PROPOSED new method Bio::Range->offsetStranded   Cook, Malcolm
  • [Bioperl-l] PROPOSED new method Bio::Range->offsetStranded   Chris Fields
• [Bioperl-l] Generalized _setparams proposal   Sendu Bala
  • [Bioperl-l] Generalized _setparams proposal   Chris Fields
    • [Bioperl-l] Generalized _setparams proposal   Sendu Bala
      • [Bioperl-l] Generalized _setparams proposal   Chris Fields
• [Bioperl-l] PROPOSED new method Bio::Range->offsetStranded   Cook, Malcolm
  • [Bioperl-l] PROPOSED new method Bio::Range->offsetStranded   Sendu Bala
    • [Bioperl-l] PROPOSED new method Bio::Range->offsetStranded   Chris Fields
• [Bioperl-l] bp_seqfeature_load of latest Flybase GFF annotationfails due to data inconsistency.   Cook, Malcolm
• [Bioperl-l] Taxon id null with load_seqdatabase.pl   George Heller
  • [Bioperl-l] Taxon id null with load_seqdatabase.pl   Brian Osborne
  • [Bioperl-l] Taxon id null with load_seqdatabase.pl   Hilmar Lapp
• [Bioperl-l] parser for BLAT cDNA-genome alignment in Sim4 format   Hong Xu
  • [Bioperl-l] parser for BLAT cDNA-genome alignment in Sim4 format   Jason Stajich
• [Bioperl-l] Fwd: FASTA version numbers   Nathan Haigh
• [Bioperl-l] Quote   Brian Osborne
  • [Bioperl-l] Quote   Catherine Letondal
• [Bioperl-l] Quote   Stephen Gordon Lenk
  • [Bioperl-l] Quote   Chris Fields
• [Bioperl-l] Quote   Stephen Gordon Lenk
• [Bioperl-l] Error while running load_seqdatabase.pl   Hilmar Lapp
  • [Bioperl-l] Error while running load_seqdatabase.pl   George Heller
    • [Bioperl-l] Error while running load_seqdatabase.pl   Hilmar Lapp
      • [Bioperl-l] Error while running load_seqdatabase.pl   George Heller
      • [Bioperl-l] Error while running load_seqdatabase.pl   Hilmar Lapp
      • [Bioperl-l] Error while running load_seqdatabase.pl   George Heller
      • [Bioperl-l] Error while running load_seqdatabase.pl   Hilmar Lapp
      • [Bioperl-l] Error while running load_seqdatabase.pl   George Heller
      • [Bioperl-l] Error while running load_seqdatabase.pl   Hilmar Lapp
      • [Bioperl-l] Error while running load_seqdatabase.pl   George Heller
• [Bioperl-l] Annotation method help   lidaof
• [Bioperl-l] Bio::Root::Root/Bio::LiveSeq::Mutation   marian thieme
  • [Bioperl-l] Bio::Root::Root/Bio::LiveSeq::Mutation   Heikki Lehvaslaiho
  • [Bioperl-l] Bio::Root::Root/Bio::LiveSeq::Mutation   Jason Stajich
• [Bioperl-l] Filehandle issue   Chris Fields
• [Bioperl-l] contig disassembly   Andrew Stewart
  • [Bioperl-l] contig disassembly   Heikki Lehvaslaiho
    • [Bioperl-l] contig disassembly   Andrew Stewart
      • [Bioperl-l] contig disassembly   Chris Fields
      • [Bioperl-l] contig disassembly   Andrew Stewart
  • [Bioperl-l] contig disassembly   Cui, Wenwu (NIH/NLM/NCBI) [C]
• [Bioperl-l] [Bioperl]problem with E-value   lidaof
  • [Bioperl-l] [Bioperl]problem with E-value   Sendu Bala
    • [Bioperl-l] [Bioperl]problem with E-value   lidaof
      • [Bioperl-l] [Bioperl]problem with E-value   Sendu Bala
      • [Bioperl-l] [Bioperl]problem with E-value   Chris Fields
      • [Bioperl-l] [Bioperl]problem with E-value   Sendu Bala
      • [Bioperl-l] [Bioperl]problem with E-value   Chris Fields
      • [Bioperl-l] [Bioperl]problem with E-value   Sendu Bala
      • [Bioperl-l] [Bioperl]problem with E-value   Chris Fields
      • [Bioperl-l] [Bioperl]problem with E-value   Chris Fields
      • [Bioperl-l] [Bioperl]problem with E-value   Chris Fields
      • [Bioperl-l] [Bioperl]problem with E-value   lidaof
      • [Bioperl-l] [Bioperl]problem with E-value   lidaof
• [Bioperl-l] error reading psi 2.5 file from intact using bioperl-network-1.5.2_100   magnusgeist
  • [Bioperl-l] error reading psi 2.5 file from intact using bioperl-network-1.5.2_100   Mikel Egaña Aranguren
    • [Bioperl-l] error reading psi 2.5 file from intact using bioperl-network-1.5.2_100   Brian Osborne
    • [Bioperl-l] Another error reading psi 1 file from intact using bioperl-network-1.5.2_100   Mikel Egaña Aranguren
      • [Bioperl-l] Another error reading psi 1 file from intact using bioperl-network-1.5.2_100   Brian Osborne
  • [Bioperl-l] error reading psi 2.5 file from intact using bioperl-network-1.5.2_100   Brian Osborne
• [Bioperl-l] Alignment->slice() issue?   Kevin Brown
  • [Bioperl-l] Alignment->slice() issue?   Kevin Brown
• [Bioperl-l] Mutation IO   marian thieme
  • [Bioperl-l] Mutation IO   Heikki Lehvaslaiho
    • [Bioperl-l] Mutation IO   Chris Fields
      • [Bioperl-l] Mutation IO   Mauricio Herrera Cuadra
      • [Bioperl-l] Mutation IO   Chris Fields
• [Bioperl-l] Translate sequences align and reverse translate   Anthony Underwood
  • [Bioperl-l] Translate sequences align and reverse translate   Roy Chaudhuri
  • [Bioperl-l] Translate sequences align and reverse translate   Albert Vilella
  • [Bioperl-l] Translate sequences align and reverse translate   Jason Stajich
• [Bioperl-l] Graphics help   Kevin Brown
  • [Bioperl-l] Graphics help   Jonathan Crabtree
• [Bioperl-l] Fwd: Bio::SearchIO::Writer::HTMLResultWriter problem   Jason Stajich
• [Bioperl-l] Bio::SearchIO::Writer::HTMLResultWriter problem   "Antonio J. Pérez"
• [Bioperl-l] ClustalW on Bioperl   Yuval Itan
• [Bioperl-l] Model deletions   marian thieme
• [Bioperl-l] ncbi blastn problem.   Cristian Gary
  • [Bioperl-l] ncbi blastn problem.   Chris Fields
• [Bioperl-l] Bio::Tree development   Johan Viklund
  • [Bioperl-l] Bio::Tree development   Sendu Bala
    • [Bioperl-l] Bio::Tree development   Chris Fields
      • [Bioperl-l] Bio::Tree development   Lucia Peixoto
      • [Bioperl-l] Bio::Tree development   Chris Fields
      • [Bioperl-l] Bio::Tree development   Jason Stajich
  • [Bioperl-l] Bio::Tree development   Hilmar Lapp
• [Bioperl-l] Parsing CDD Results?   Andy Lindeman
  • [Bioperl-l] Parsing CDD Results?   Jason Stajich
    • [Bioperl-l] Parsing CDD Results?   Torsten Seemann
      • [Bioperl-l] Parsing CDD Results?   Chris Fields
      • [Bioperl-l] missing test file(s)   Erik
      • [Bioperl-l] missing test file(s)   Chris Fields
      • [Bioperl-l] missing test file(s)   Weigang Qiu
      • [Bioperl-l] missing test file(s)   Chris Fields
  • [Bioperl-l] Parsing CDD Results?   Chris Fields
• [Bioperl-l] Bio/SeqFeature/Annotated proposed patch   Cook, Malcolm
  • [Bioperl-l] Bio/SeqFeature/Annotated proposed patch   Chris Fields
  • [Bioperl-l] Bio/SeqFeature/Annotated proposed patch   Sendu Bala
• [Bioperl-l] proposed patch to Bio/Annotation/SimpleValue.pm   Cook, Malcolm
• [Bioperl-l] Bio/SeqFeature/Annotated proposed patch   Cook, Malcolm
• [Bioperl-l] wikipedia-ers   Jason Stajich
  • [Bioperl-l] wikipedia-ers   Sendu Bala
    • [Bioperl-l] wikipedia-ers   Mauricio Herrera Cuadra
      • [Bioperl-l] wikipedia-ers   Sendu Bala
      • [Bioperl-l] wikipedia-ers   Chris Fields
• [Bioperl-l] constant Graphics height   Brent Pedersen
  • [Bioperl-l] constant Graphics height   Brent Pedersen
• [Bioperl-l] human_small-01.xml file   Brian Osborne
• [Bioperl-l] bioperl-network-1.5.2_100 node IDs   Mikel Egaña Aranguren
  • [Bioperl-l] bioperl-network-1.5.2_100 node IDs   Brian Osborne
• [Bioperl-l] Finding coding sequences corresponding to protein sequences   Warren Gallin
• [Bioperl-l] Bio::DB::SeqFeature::Store issues   Sendu Bala
  • [Bioperl-l] Bio::DB::SeqFeature::Store issues   Lincoln Stein
• [Bioperl-l] Is there any solution to residue leak problem of the Bio::Structure::Entry get_residues() method   Jian Huang
  • [Bioperl-l] Is there any solution to residue leak problem of the Bio::Structure::Entry get_residues() method   Chris Fields
    • [Bioperl-l] Is there any solution to residue leak problem of the Bio::Structure::Entry get_residues() method   Jian Huang
      • [Bioperl-l] Is there any solution to residue leak problem of the Bio::Structure::Entry get_residues() method   Chris Fields
      • [Bioperl-l] Is there any solution to residue leak problem of the Bio::Structure::Entry get_residues() method   Jian Huang
• [Bioperl-l] bioperl-microarray: status?   Jay Hannah
  • [Bioperl-l] bioperl-microarray: status?   Allen Day
    • [Bioperl-l] bioperl-microarray: status?   Jay Hannah
      • [Bioperl-l] bioperl-microarray: status?   Chris Fields
• [Bioperl-l] Pathway tools output parser   Jim Hu
• [Bioperl-l] Species name problems with bioperl-db   Roy Chaudhuri
  • [Bioperl-l] Species name problems with bioperl-db   Sendu Bala
• [Bioperl-l] bp_genbank2gff3.pl   Eric Just
• [Bioperl-l] to_FTstring() for Bio::Graphics::FeatureBase   Lincoln Stein
  • [Bioperl-l] to_FTstring() for Bio::Graphics::FeatureBase   Jason Stajich
• [Bioperl-l] swissprot stream with no ID. Not swissprot in my book   Michael Gore
  • [Bioperl-l] swissprot stream with no ID. Not swissprot in my book   Chris Fields
    • [Bioperl-l] swissprot stream with no ID. Not swissprot in my book   Michael Gore
• [Bioperl-l] Downloading the tutorial for offline reading   Michiel Jan Laurens de Hoon
  • [Bioperl-l] Downloading the tutorial for offline reading   Brian Osborne
    • [Bioperl-l] Downloading the tutorial for offline reading   Chris Fields
      • [Bioperl-l] Downloading the tutorial for offline reading   Brian Osborne
      • [Bioperl-l] DocBook docs, was Re: Downloading the tutorial for offline reading   Chris Fields
      • [Bioperl-l] DocBook docs, was Re: Downloading the tutorial for offline reading   Brian Osborne
      • [Bioperl-l] DocBook docs, was Re: Downloading the tutorial for offline reading   Chris Fields
• [Bioperl-l] Bug in the Bio::SeqIO.scf.pm code   Anthony Underwood
  • [Bioperl-l] Bug in the Bio::SeqIO.scf.pm code   Chris Fields
• [Bioperl-l] Hyphy::REL code example   Albert Vilella
• [Bioperl-l] Bio::DB::SeqFeature treamtent of tags and annotations   Cook, Malcolm
  • [Bioperl-l] Bio::DB::SeqFeature treamtent of tags and annotations   Lincoln Stein
• [Bioperl-l] "jump" to the right sequence in a SeqIO object   zhihua li
  • [Bioperl-l] "jump" to the right sequence in a SeqIO object   Torsten Seemann
    • [Bioperl-l] "jump" to the right sequence in a SeqIO object   Brian Osborne
  • [Bioperl-l] "jump" to the right sequence in a SeqIO object   Chris Fields
• [Bioperl-l] CON(structed) sequence databases?   JK (Jesper Agerbo Krogh)
  • [Bioperl-l] CON(structed) sequence databases?   Chris Fields
• [Bioperl-l] BLASTXML XML::SAX::Expat issues resolved   Chris Fields
• [Bioperl-l] to_FTstring() for Bio::Graphics::FeatureBase   Lincoln Stein
• [Bioperl-l] ActivePerl 5.8.8.820 Release   Nathan Haigh
• [Bioperl-l] Bio::DB::SeqFeature treamtent of tags and annotations   Cook, Malcolm
  • [Bioperl-l] Bio::DB::SeqFeature treamtent of tags and annotations   Lincoln Stein
• [Bioperl-l] your kind help needed!   xiefuliang
  • [Bioperl-l] your kind help needed!   Sendu Bala
• [Bioperl-l] want score from needle output   neeti somaiya
  • [Bioperl-l] want score from needle output   Chris Fields
• [Bioperl-l] Bio::DB::SeqFeature::Store delete() not working   Sendu Bala
  • [Bioperl-l] Bio::DB::SeqFeature::Store delete() not working   Sendu Bala
    • [Bioperl-l] Bio::DB::SeqFeature::Store delete() not working   Lincoln Stein
• [Bioperl-l] Bio::DB::SeqFeature::Store delete() not working   Cook, Malcolm
• [Bioperl-l] bioperl-db Species question   Chris Fields
• [Bioperl-l] How to get from gi/ref/gb to genomic coordinates ?   Rainer Machne
  • [Bioperl-l] How to get from gi/ref/gb to genomic coordinates ?   Jason Stajich
  • [Bioperl-l] How to get from gi/ref/gb to genomic coordinates ?   Barry Moore

Last message date: Wed Jan 31 23:27:30 UTC 2007
Archived on: Mon Jun 16 02:47:46 UTC 2014

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