August 2005 Archives by thread

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Starting: Mon Aug 1 09:03:09 EST 2005
Ending: Wed Aug 31 19:34:54 EST 2005
Messages: 203

• [Bioperl-l] Patching lucy   Andrew Walsh
  • [Bioperl-l] Patching lucy   Phillip San Miguel
    • [Bioperl-l] Patching lucy   Andrew Walsh
      • [Bioperl-l] Patching lucy   Phillip San Miguel
• [Bioperl-l] retrieving medline citations   Nathan Haigh
• [Bioperl-l] Newbie gbrowse help - script to make gff from fasta   Scott Cain
  • [Bioperl-l] Newbie gbrowse help - script to make gff from fasta   Scott Cain
• [Bioperl-l] ABI average singal intensity   Xiaojun Hu
  • [Bioperl-l] ABI average singal intensity   Phillip San Miguel
• [Bioperl-l] Connecting to Bio::DB::GFF db   Andrew Nunberg
  • [Bioperl-l] Connecting to Bio::DB::GFF db   Scott Cain
• [Bioperl-l] Re: Fixing bioperl [was Re: Analysis features]   Scott Cain
  • [Bioperl-l] Re: Fixing bioperl [was Re: Analysis features]   Hilmar Lapp
    • [Bioperl-l] all tests pass [was Re: Fixing bioperl] [was Re: Analysis features]   Jason Stajich
      • [Bioperl-l] Re: all tests pass [was Re: Fixing bioperl] [was Re: Analysis features]   Hilmar Lapp
• [Bioperl-l] Bioinformatics Software Development Survey   HASE
• [Bioperl-l] Bug in Bio::SeqFeature::Annotated ?   Emmanuel QUEVILLON
• [Bioperl-l] parse genbank file   Guido Dieterich
  • [Bioperl-l] parse genbank file   Andrew Walsh
• [Bioperl-l] Bio::Tools::Run::PiseApplication : parameters changes in seqgen   Catherine Letondal
• [Bioperl-l] Bio::Tools::Run prepare executions [was Re:bioperl-run Codeml.pm fix_blength]   Albert Vilella
  • [Bioperl-l] Re: Bio::Tools::Run prepare executions [was Re:bioperl-run Codeml.pm fix_blength]   Jason Stajich
• [Bioperl-l] Error making query to Bio::DB:GFF db   Andrew Nunberg
• [Bioperl-l] bl2seq and next_aln()   Gregory Drake Wilson
  • [Bioperl-l] bl2seq and next_aln()   Jason Stajich
• [Bioperl-l] newbie Q - missing Tools/HMM.pm ?   radev at umich.edu
  • [Bioperl-l] newbie Q - missing Tools/HMM.pm ?   Sean Davis
  • [Bioperl-l] newbie Q - missing Tools/HMM.pm ?   Jason Stajich
• [Bioperl-l] darwin PERL5LIB ignored   Allen Day
  • [Bioperl-l] darwin PERL5LIB ignored   Tim Erwin
    • bioperl rpms via yum on Darwin (Was: [Bioperl-l] darwin PERL5LIB ignored0   Allen Day
    • [Bioperl-l] get_Seq_by_id question   Niels Larsen
      • [Bioperl-l] get_Seq_by_id question   Heikki Lehvaslaiho
      • [Bioperl-l] get_Seq_by_id question   Heikki Lehvaslaiho
• [Bioperl-l] bl2seq   Usha
• [Bioperl-l] bl2seq   Usha Rani Reddi
  • [Bioperl-l] bl2seq   James Wasmuth
• [Bioperl-l] dividing seqboot outfiles   matthieu
  • [Bioperl-l] dividing seqboot outfiles   Jason Stajich
• [Bioperl-l] dividing seqboot outfile   matthieu
• [Bioperl-l] search2gff.PLS   Hilmar Lapp
• [Bioperl-l] Not picking up Dbxrefs EMBL records   SG Edwards
  • [Bioperl-l] Not picking up Dbxrefs EMBL records   Hilmar Lapp
    • [Bioperl-l] Not picking up Dbxrefs EMBL records   SG Edwards
      • [Bioperl-l] Not picking up Dbxrefs EMBL records   Hilmar Lapp
• [Bioperl-l] local electric charge/hydrophobicity/flexibility of proteins   Tamas Horvath
• [Bioperl-l] new modules for sarching for patterns in fasta-files   markus.riester at student.uni-tuebingen.de
  • [Bioperl-l] new modules for sarching for patterns in fasta-files   Aaron J. Mackey
    • [Bioperl-l] new modules for sarching for patterns in fasta-files   markus.riester at student.uni-tuebingen.de
      • [Bioperl-l] new modules for sarching for patterns in fasta-files   markus.riester at student.uni-tuebingen.de
• [Bioperl-l] Bioperl version string not picked up by MakeMaker   lstein at cshl.edu
  • [Bioperl-l] Bioperl version string not picked up by MakeMaker   Aaron J. Mackey
  • [Bioperl-l] Bioperl version string not picked up by MakeMaker   Jason Stajich
• [Bioperl-l] Question about handling ontology files   iluminati at earthlink.net
  • [Bioperl-l] Question about handling ontology files   Sean Davis
    • [Bioperl-l] Question about handling ontology files   Sean Davis
• [Bioperl-l] [Bioperl -l] Problem reading EMBL format file   Iain Wallace
  • [Bioperl-l] [Bioperl -l] Problem reading EMBL format file   Hans Rudolf Hotz
• [Bioperl-l] embl sequences 2 fasta   Pedro Antonio Reche
• [Bioperl-l] Bio::DB::Taxonomy::entrez updated   Jason Stajich
• [Bioperl-l] new modules for sarching for patterns in fasta-fi les   Amir Karger
  • [Bioperl-l] new modules for sarching for patterns in fasta-fi les   Heikki Lehvaslaiho
• [Bioperl-l] Extract Mutation Automatically   Andrew Leung
  • [Bioperl-l] Extract Mutation Automatically   Jason Stajich
    • [Bioperl-l] calculating the Ka/Ks ratio   Darren Obbard
      • [Bioperl-l] calculating the Ka/Ks ratio   Albert Vilella
      • [Bioperl-l] calculating the Ka/Ks ratio   Csaba Ortutay
    • [Bioperl-l] Extract Mutation Automatically   Andrew Leung
      • [Bioperl-l] Extract Mutation Automatically   Jason Stajich
      • [Bioperl-l] Extract Mutation Automatically   Andrew Leung
      • [Bioperl-l] Extract Mutation Automatically   Jason Stajich
      • [Bioperl-l] Extract Mutation Automatically   Heikki Lehvaslaiho
      • [Bioperl-l] Extract Mutation Automatically   Andrew Leung
      • [Bioperl-l] Extract Mutation Automatically   Heikki Lehvaslaiho
• [Bioperl-l] Bio::SeqFeature::OntologyTypedI Proposal   Ewan Birney
  • [Bioperl-l] Bio::SeqFeature::OntologyTypedI Proposal   Aaron J. Mackey
  • [Bioperl-l] Re: Bio::SeqFeature::OntologyTypedI Proposal   Chris Mungall
    • [Bioperl-l] Re: Bio::SeqFeature::OntologyTypedI Proposal   Hilmar Lapp
      • [Bioperl-l] Re: Bio::SeqFeature::OntologyTypedI Proposal   Ewan Birney
      • [Bioperl-l] Re: Bio::SeqFeature::OntologyTypedI Proposal   Chris Mungall
      • [Bioperl-l] Re: Bio::SeqFeature::OntologyTypedI Proposal   Hilmar Lapp
• [Bioperl-l] Re: Feature-Annotation HOWTO   Brian Osborne
• [Bioperl-l] Extract Mutation Automatically   Cook, Malcolm
• [Bioperl-l] Return $hit->name by Score Bit value when parsing blast result   Andrew Leung
  • [Bioperl-l] Return $hit->name by Score Bit value when parsing blast result   Jason Stajich
• [Bioperl-l] Re: Bioperl-l Digest, Vol 28, Issue 6   Rambabu Gudavalli
• [Bioperl-l] download popset file using bioperl   Rambabu Gudavalli
• [Bioperl-l] where to discuss namespaces for modules?   markus.riester at student.uni-tuebingen.de
• [Bioperl-l] Windows bug in Bio::DB::Fasta?   Scott Cain
  • [Bioperl-l] Windows bug in Bio::DB::Fasta?   Scott Cain
    • [Bioperl-l] Windows bug in Bio::DB::Fasta?   Lincoln Stein
      • [Bioperl-l] Windows bug in Bio::DB::Fasta?   Chris Fields
      • [Gmod-gbrowse] Re: [Bioperl-l] Windows bug in Bio::DB::Fasta?   Lincoln Stein
• [Bioperl-l] Bio::Align::AlignI for EMBOSS:needle   Ryan Golhar
  • [Bioperl-l] Bio::Align::AlignI for EMBOSS:needle   Jason Stajich
    • [Bioperl-l] Bio::Align::AlignI for EMBOSS:needle   Ryan Golhar
• [Bioperl-l] GuessSeqFormat problems   Jason Stajich
  • [Bioperl-l] Re: GuessSeqFormat problems   Albert Vilella
    • [Bioperl-l] Re: GuessSeqFormat problems   Andreas Kahari
      • [Bioperl-l] Re: GuessSeqFormat problems   Andreas Kahari
      • [Bioperl-l] Re: GuessSeqFormat problems   Albert Vilella
      • [Bioperl-l] Another GuessSeqFormat question   Tim Erwin
      • [Bioperl-l] Another GuessSeqFormat question   Heikki Lehvaslaiho
      • [Bioperl-l] Another GuessSeqFormat question   Tim Erwin
      • [Bioperl-l] Another GuessSeqFormat question   Heikki Lehvaslaiho
• [Bioperl-l] new modules for sarching for patterns in fasta-fi les   Amir Karger
• [Bioperl-l] Announce: Bio::Seq::Quality   Heikki Lehvaslaiho
• [Bioperl-l] A question about the perl code   Alex Zhang
  • [Bioperl-l] A question about the perl code   Johan Viklund
• [Bioperl-l] thanks for the hardwork on HOWTO changeover   Jason Stajich
  • [Bioperl-l] Re: thanks for the hardwork on HOWTO changeover   Brian Osborne
• [Bioperl-l] A question about the perl code   Amir Karger
• [Bioperl-l] Problems using Bio::Ext::Align and Bio::SeqIO::staden::read   Bryan Yi
• [Bioperl-l] Trouble with Bio::Graphics   michael watson (IAH-C)
  • [Bioperl-l] Trouble with Bio::Graphics   Scott Cain
• [Bioperl-l] Trouble with Bio::Graphics   michael watson (IAH-C)
• [Bioperl-l] Multiline Query Name in Blast Output   Waibhav Tembe
  • [Bioperl-l] Multiline Query Name in Blast Output   Jason Stajich
    • [Bioperl-l] Multiline Query Name in Blast Output   Waibhav Tembe
      • [Bioperl-l] Multiline Query Name in Blast Output   Jason Stajich
• [Bioperl-l] Bio::DB::GFF::Adaptor::berkeleydb   Jason Stajich
  • [Bioperl-l] Bio::DB::GFF::Adaptor::berkeleydb   Jason Stajich
    • [Bioperl-l] Bio::DB::GFF::Adaptor::berkeleydb   Lincoln Stein
    • [Bioperl-l] Bio::DB::GFF::Adaptor::berkeleydb   Lincoln Stein
  • [Bioperl-l] Bio::DB::GFF::Adaptor::berkeleydb   Lincoln Stein
• [Bioperl-l] write sequence into file after stream query to database   chen li
• [Bioperl-l] Re: [BioSQL-l] loading fasta records with load_seqdatabase.pl - correct fasta headers   Hilmar Lapp
• [Bioperl-l] [OT] ISO guide to human genomics DBs   kynn at panix.com
  • [Bioperl-l] [OT] ISO guide to human genomics DBs   Stefan Kirov
• [Bioperl-l] [OT] ISO guide to human genomics DBs   Horvath, Monica (NIH/NIEHS)
• [Bioperl-l] bl2seq   Usha Rani Reddi
  • [Bioperl-l] bl2seq   James Wasmuth
  • [Bioperl-l] bl2seq   Paulo Almeida
• [Bioperl-l] Re: [BioSQL-l] loading fasta records with load_seqdatabase.pl - correct fasta headers   mark.schreiber at novartis.com
  • [Bioperl-l] Re: [BioSQL-l] loading fasta records with load_seqdatabase.pl - correct fasta headers   Hilmar Lapp
• [Bioperl-l] Local bl2seq   Usha Rani Reddi
• [Bioperl-l] Bio::DB::GFF, aggregators, and spliced_seq   Gathman, Allen
• [Bioperl-l] RE: Local bl2seq   Barry Moore
• [Bioperl-l] Strange result   thechans at citiz.net
  • [Bioperl-l] Strange result   Barry Moore
    • [Bioperl-l] Strange result   Ewan Birney
      • [Bioperl-l] Strange result   Hilmar Lapp
• [Bioperl-l] Re: Thanks   Barry Moore
  • [Bioperl-l] Re: Thanks   Hilmar Lapp
• [Bioperl-l] maximum likelihood estimation   Arne Nolte
  • [Bioperl-l] maximum likelihood estimation   Ed Green
• [Bioperl-l] Bio::DB::GFF, aggregators, and spliced_seq   Allen Gathman
• [Bioperl-l] 1.5.1 todo list   Jason Stajich
  • [Bioperl-l] 1.5.1 todo list   Ewan Birney
    • [Bioperl-l] 1.5.1 todo list   Lincoln Stein
  • [Bioperl-l] 1.5.1 todo list   Hilmar Lapp
• [Bioperl-l] TypedSeqFeatureI is in; tests which fail   Ewan Birney
  • [Bioperl-l] TypedSeqFeatureI is in; tests which fail   Jason Stajich
    • [Bioperl-l] TypedSeqFeatureI is in; tests which fail   Ewan Birney
      • [Bioperl-l] TypedSeqFeatureI is in; tests which fail   Hilmar Lapp
      • [Bioperl-l] TypedSeqFeatureI is in; tests which fail   Ewan Birney
• [Bioperl-l] [OT] General bioinformatics forums/lists?   kynn at panix.com
  • [Bioperl-l] [OT] General bioinformatics forums/lists?   sumit middha
• [Bioperl-l] DocBook Question   Barry Moore
• [Bioperl-l] Bio::DB::GFF start/end coordinates   Jason Stajich
  • [Bioperl-l] Re: Bio::DB::GFF start/end coordinates   Lincoln Stein
• [Bioperl-l] [OT] General bioinformatics forums/lists?   Goel, Manisha
• [Bioperl-l] ->add_tag_value()   Andrew Stewart
  • [Bioperl-l] ->add_tag_value()   Jason Stajich
  • [Bioperl-l] ->add_tag_value()   Allen Day
• [Bioperl-l] DBI connection parameters and BasePersistenceAdaptor.pm   Amit Indap
  • [Bioperl-l] DBI connection parameters   Hilmar Lapp
• [Bioperl-l] DocBook Question   Tristan Fiedler
• [Bioperl-l] How to generate negative pair for motif binding sites in Perl?   Alex Zhang
• [Bioperl-l] How do I tell what version of bioperl is installed?   Wes Barris
  • [Bioperl-l] How do I tell what version of bioperl is installed?   Jason Stajich
• [Bioperl-l] RE: Bioperl-l Digest, Vol 28, Issue 10   Barry Moore
• [Bioperl-l] ->add_tag_value()   Jason Stajich
  • [Bioperl-l] ->add_tag_value()   Hilmar Lapp
    • [Bioperl-l] ->add_tag_value()   Andrew Stewart
      • [Bioperl-l] ->add_tag_value()   Lincoln Stein
      • [Bioperl-l] ->add_tag_value()   Hilmar Lapp
• [Bioperl-l] bug report - SeqIO::genbank.pm   Qunfeng
  • [Bioperl-l] bug report - SeqIO::genbank.pm   Brian Osborne
• [Bioperl-l] ontology paths in Bioperl-DB / Biosql   Hilmar Lapp
• [Bioperl-l] [OT] General bioinformatics forums/lists?   hong kong pm
  • [Bioperl-l] [OT] General bioinformatics forums/lists?   Boris Steipe
• [Bioperl-l] Bio::Search results   Sean O'Keeffe
• [Bioperl-l] If you use RemoteBlast   Jason Stajich
  • [Bioperl-l] If you use RemoteBlast   Paulo Almeida
• [Bioperl-l] Re: [Gmod-gbrowse] GTF-->GFF3 converter   Scott Cain
• [Bioperl-l] If you use RemoteBlast   Barry Moore
• [Bioperl-l] Bio::Search results   Sean O'Keeffe
• [Bioperl-l] SO for RNA-Binding Protein and RNA motifs   Chris Fields
• [Bioperl-l] Bio::Search results   Barry Moore
  • [Bioperl-l] Bio::Search results   Sean O'Keeffe
• [Bioperl-l] get_sequence - acc does not exist   Paul G Cantalupo
  • [Bioperl-l] get_sequence - acc does not exist   Ewan Birney
• [Bioperl-l] Make test fails   Ryan Golhar
  • [Bioperl-l] Make test fails   Jason Stajich
• [Bioperl-l] interoperability with bioperl   Rutger Vos
  • [Bioperl-l] interoperability with bioperl   Ewan Birney
• [Bioperl-l] Protein alignment CD excision module   Stephen Gordon Lenk
  • [Bioperl-l] Protein alignment CD excision module   Heikki Lehvaslaiho
• [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Cook, Malcolm
• [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Jason Stajich
• [Bioperl-l] Alignment excision script   Stephen Gordon Lenk
• [Bioperl-l] Bioperl adds utility to msaexcise script   Stephen Gordon Lenk

Last message date: Wed Aug 31 19:34:54 EST 2005
Archived on: Wed Aug 31 20:24:12 EST 2005

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