April 2005 Archives by thread

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Starting: Fri Apr 1 03:52:10 EST 2005
Ending: Fri Apr 29 15:44:41 EST 2005
Messages: 276

• [Bioperl-l] EntrezGene ASN parser   Hilmar Lapp
  • [Bioperl-l] EntrezGene ASN parser   Stefan Kirov
• [Bioperl-l] patch to FeatureIO.pm for tied interface   Hilmar Lapp
• [Bioperl-l] pubmed   Hilmar Lapp
  • [Bioperl-l] pubmed   Paulo Almeida
• [Bioperl-l] Export a list of genes containing this family   Irshad Khan
  • [Bioperl-l] Export a list of genes containing this family   Paulo Almeida
• [Bioperl-l] Easy switching from wwwBlast to QBlast - Wrong CVS diff   Madeleine Lemieux
• [Bioperl-l] Help with taxonomy db   Brian Osborne
  • [Bioperl-l] Help with taxonomy db   Jason Stajich
    • [Bioperl-l] Help with taxonomy db   Brian Osborne
• [Bioperl-l] Turning the tree into bifurcating one   Jason Stajich
• [Bioperl-l] INSECT Cluster and RAID   Scott Lambdin
• [Bioperl-l] pubmed   Hilmar Lapp
  • [Bioperl-l] pubmed   Qunfeng
    • [Bioperl-l] pubmed   Brian Osborne
      • [Bioperl-l] pubmed   Qunfeng
      • [Bioperl-l] pubmed   Brian Osborne
      • [Bioperl-l] pubmed   Qunfeng
      • [Bioperl-l] pubmed   Brian Osborne
      • [Bioperl-l] pubmed   Qunfeng
      • [Bioperl-l] pubmed   Jason Stajich
• [Bioperl-l] Bio::Index:EMBL on embl flatfiles   Jonathan Miller
  • [Bioperl-l] Re: Bio::Index:EMBL on embl flatfiles   Jonathan Miller
  • [Bioperl-l] Bio::Index:EMBL on embl flatfiles   Brian Osborne
  • [Bioperl-l] newbie needs help with "preferred_id_type"   Jonathan Miller
    • [Bioperl-l] Re: newbie needs help with read/write Genbank   Jonathan Miller
      • [Bioperl-l] Re: newbie needs help with read/write Genbank   Hilmar Lapp
    • [Bioperl-l] newbie needs help with "preferred_id_type"   Andrew Walsh
• [Bioperl-l] two sequences alignment question   yanfeng
  • [Bioperl-l] two sequences alignment question   Jason Stajich
• [Bioperl-l] Bio::LocationI Interface   Suhas Tikole
• [Bioperl-l] Re: BIo::LocationI Interface   Jason Stajich
• [Bioperl-l] Sorting BLAST Output   Waibhav Tembe
  • [Bioperl-l] Sorting BLAST Output   Andrew Walsh
    • [Bioperl-l] Sorting BLAST Output   Terry Jones
• [Bioperl-l] drawing additional axes with GD::Graph   Lincoln Stein
• [Bioperl-l] Re: Thank you for your reply.   Jason Stajich
• [Bioperl-l] Bio::Index:EMBL on embl flatfiles   Brian Osborne
• [Bioperl-l] Query sequence length <= 0   Yanfeng Shi
  • [Bioperl-l] Query sequence length <= 0   Brian Osborne
• [Bioperl-l] newbie needs help with "preferred_id_type"   Cook, Malcolm
  • [Bioperl-l] newbie needs help with "preferred_id_type"   Hilmar Lapp
    • [Bioperl-l] newbie needs help with "preferred_id_type"   Jonathan Miller
      • [Bioperl-l] newbie needs help with "preferred_id_type"   Jason Stajich
• [Bioperl-l] Entrezgene parser: new parser available from sourceforge (attached too) (fwd)   Stefan A Kirov
  • [Bioperl-l] Entrezgene parser: new parser available from sourceforge (attached too) (fwd)   Brian Osborne
    • [Bioperl-l] Entrezgene parser: new parser available from sourceforge (attached too) (fwd)   Stefan Kirov
    • [Bioperl-l] Entrezgene parser: new parser available from sourceforge (attached too) (fwd)   Hilmar Lapp
      • [Bioperl-l] Entrezgene parser: new parser available from sourceforge (attached too) (fwd)   Stefan Kirov
• [Bioperl-l] newbie needs help with "preferred_id_type"   Hilmar Lapp
• [Bioperl-l] Getting description of BLAST hits   Peter.Robinson at t-online.de
  • [Bioperl-l] Getting description of BLAST hits   Jason Stajich
    • [Bioperl-l] Getting description of BLAST hits   Peter.Robinson at t-online.de
• [Bioperl-l] Blast Connection Error   박준형
• [Bioperl-l] Bio::Seq::PrimedSeq::new exception   Mike Muratet
• [Bioperl-l] Getting description of BLAST hits   Marc Logghe
  • [Bioperl-l] Getting description of BLAST hits   Peter.Robinson at t-online.de
• [Bioperl-l] FW: Help with hmmpfam   Kary Ann Del Carmen Soriano Ocana
• [Bioperl-l] patch to FeatureIO.pm for tied interface   Cook, Malcolm
• [Bioperl-l] RE: Problem running clustalw.pl for the first time.   Lisa
  • [Bioperl-l] RE: Problem running clustalw.pl for the first time.   Scott Cain
• [Bioperl-l] biosql.html   Brian Osborne
  • [Bioperl-l] biosql.html   Hilmar Lapp
• [Bioperl-l] Bio::Search::Hit   Mike Muratet
  • [Bioperl-l] Bio::Search::Hit   Jason Stajich
    • [Bioperl-l] Bio::Search::Hit   Mike Muratet
• [Bioperl-l] RE: Problem running clustalw.pl for the first time.   Scott Cain
• [Bioperl-l] Entrez Gene parser   Stefan Kirov
  • [Bioperl-l] Entrez Gene parser   Brian Osborne
    • [Bioperl-l] Entrez Gene parser   Stefan Kirov
  • [Bioperl-l] Entrez Gene parser   Hilmar Lapp
    • [Bioperl-l] Entrez Gene parser   Stefan Kirov
      • [Bioperl-l] Entrez Gene parser   Mingyi Liu
    • [Bioperl-l] overloading of methods and ptkdb   Stefan Kirov
      • [Bioperl-l] overloading of methods and ptkdb   Hilmar Lapp
• [Bioperl-l] Blast Connection Error   Madeleine Lemieux
• [Bioperl-l] single NHX treefile from two phylip files   W.Kenworthy
  • [Bioperl-l] single NHX treefile from two phylip files   Jason Stajich
• [Bioperl-l] CFP NETTAB 2005: Network Tools and Applications in Biology / Workflows management   Catherine Letondal
• [Bioperl-l] Problem with Bio::DB::GFF   Gathman, Allen
  • [Bioperl-l] Problem with Bio::DB::GFF   Lincoln Stein
• [Bioperl-l] obtaining nt seqs using protein GI's   Nathan Spencer Haigh
  • [Bioperl-l] obtaining nt seqs using protein GI's   Jason Stajich
• [Bioperl-l] SeqIO::table   Hilmar Lapp
  • [Bioperl-l] SeqIO::table   Brian Osborne
    • [Bioperl-l] UniGene   badr al-daihani
      • [Bioperl-l] UniGene   Sean Davis
• [Bioperl-l] Reminder: Yet Another Perl Conference in Toronto, June 27 - 29   Gerard Lim
• [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   CHANDAN SINGH
• FW: [Bioperl-l] FW: Help with hmmpfam   Kary Ann Del Carmen Soriano Ocana
• [Bioperl-l] FW: Help with hmmpfam   Marc Logghe
• [Bioperl-l] FW: Help with hmmpfam   Kary Ann Del Carmen Soriano Ocana
• [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   Madeleine Lemieux
• [Bioperl-l] Bio::AlignIO error   Alex Brown
  • [Bioperl-l] Bio::AlignIO error   Jason Stajich
• [Bioperl-l] Re: Entrez gene parser code   Stefan Kirov
  • [Bioperl-l] Re: Entrez gene parser code   Mingyi Liu
    • [Bioperl-l] Re: Entrez gene parser code   Stefan Kirov
      • [Bioperl-l] Re: Entrez gene parser code   Mingyi Liu
      • [Bioperl-l] Re: Entrez gene parser code   Hilmar Lapp
      • [Bioperl-l] Re: Entrez gene parser code   Jason Stajich
      • [Bioperl-l] Re: Entrez gene parser code   Mingyi Liu
    • [Bioperl-l] Re: Entrez gene parser code   Colin Erdman
      • [Bioperl-l] Re: Entrez gene parser code   Stefan Kirov
      • [Bioperl-l] Bio::ASN1::EntrezGene available on CPAN now   Mingyi Liu
      • [Bioperl-l] Re: Entrez gene parser code   Brian Osborne
      • [Bioperl-l] Re: Entrez gene parser code   Barry Moore
• [Bioperl-l] bioperl1.5 generate_cigar_string   Susan J. Miller
  • [Bioperl-l] bioperl1.5 generate_cigar_string   Jason Stajich
    • [Bioperl-l] SearchIO::Writer::GbrowseGFF   Susan J. Miller
      • [Bioperl-l] SearchIO::Writer::GbrowseGFF   Jason Stajich
• [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   Madeleine Lemieux
  • [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   CHANDAN SINGH
    • [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   CHANDAN SINGH
      • [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   Madeleine Lemieux
• [Bioperl-l] why does Bio::Tools::Run::Hmmer return a SearchIO object for hmmalign?   Scott Markel
  • [Bioperl-l] why does Bio::Tools::Run::Hmmer return a SearchIO object for hmmalign?   Jason Stajich
    • [Bioperl-l] why does Bio::Tools::Run::Hmmer return a SearchIO object for hmmalign?   Scott Markel
      • [Bioperl-l] why does Bio::Tools::Run::Hmmer return a SearchIO object for hmmalign?   Scott Markel
• [Bioperl-l] Entrez Gene ASN.1 solution   Mark Lambrecht
  • [Bioperl-l] Entrez Gene ASN.1 solution   Stefan Kirov
• [Bioperl-l] Help with parsing (BLAST/exonerate) for DAS server   Michael Seewald
  • [Bioperl-l] Help with parsing (BLAST/exonerate) for DAS server   Will Spooner
• [Bioperl-l] How to obtain the chromosome from an Accession Number   Ryan Golhar
  • [Bioperl-l] How to obtain the chromosome from an Accession Number   Sean Davis
    • [Bioperl-l] How to obtain the chromosome from an Accession Number   Sean Davis
      • [Bioperl-l] How to obtain the chromosome from an Accession Number   Ryan Golhar
• [Bioperl-l] Entrez Gene ASN.1 solution   Colin Erdman
  • [Bioperl-l] Entrez Gene ASN.1 solution   Stefan Kirov
• [Bioperl-l] Remote::Blast   Thiago Motta Venancio
  • [Bioperl-l] Remote::Blast   CHANDAN SINGH
• [Bioperl-l] Entrez Gene ASN.1 solution   Colin Erdman
• [Bioperl-l] Newbie Questions: bioperl, bioperl-db, and GO   jjmail at mac.com
  • [Bioperl-l] Newbie Questions: bioperl, bioperl-db, and GO   Hilmar Lapp
    • [Bioperl-l] Newbie Questions: bioperl, bioperl-db, and GO   Jamie Sherman
      • [Bioperl-l] Newbie Questions: bioperl, bioperl-db, and GO   Hilmar Lapp
  • [Bioperl-l] Newbie Questions: bioperl, bioperl-db, and GO   Sean Davis
• [Bioperl-l] Entrez Gene ASN.1 solution   Mark Lambrecht
• [Bioperl-l] Entrez Gene ASN.1 solution   Mark Lambrecht
• [Bioperl-l] Bio::Graphics::Panel   Horvath Tamas
• [Bioperl-l] Very basic Perl/BioPerl Help   Colin Erdman
  • [Bioperl-l] Very basic Perl/BioPerl Help   Stefan Kirov
  • [Bioperl-l] Very basic Perl/BioPerl Help   Sean Davis
    • [Bioperl-l] Very basic Perl/BioPerl Help   Colin Erdman
      • [Bioperl-l] Very basic Perl/BioPerl Help   Terry Jones
  • [Bioperl-l] Very basic Perl/BioPerl Help   Stefan Kirov
    • [Bioperl-l] Parse::RecDescent in BioPerl and bioinformatics   Edward WIJAYA
      • [Bioperl-l] Parse::RecDescent in BioPerl and bioinformatics   Jason Stajich
      • [Bioperl-l] Parse::RecDescent in BioPerl and bioinformatics   Mingyi Liu
    • [Bioperl-l] Very basic Perl/BioPerl Help   Terry Jones
    • [Bioperl-l] Very basic Perl/BioPerl Help   Terry Jones
      • [Bioperl-l] Very basic Perl/BioPerl Help   Stefan Kirov
  • [Bioperl-l] Very basic Perl/BioPerl Help   Terry Jones
• [Bioperl-l] Bio::DB::Genbank not working after installation   Wang, Jianjun
  • [Bioperl-l] Bio::DB::Genbank not working after installation   Jason Stajich
  • [Bioperl-l] Bio::DB::Genbank not working after installation   Brian Osborne
• [Bioperl-l] Entrez parser   Stefan Kirov
  • [Bioperl-l] Entrez parser   Mingyi Liu
• [Bioperl-l] how to use Storable.pm to save the object?   Sally Li
  • [Bioperl-l] how to use Storable.pm to save the object?   Will Spooner
• [Bioperl-l] (no subject)   Khan, Sohail
  • [Bioperl-l] (no subject)   Paulo Almeida
• [Bioperl-l] Array call in Bio::AlignIO   Edward Wijaya
• [Bioperl-l] NCBI eutils BioPerl Module   Ryan Golhar
  • [Bioperl-l] NCBI eutils BioPerl Module   Hilmar Lapp
  • [Bioperl-l] NCBI eutils BioPerl Module   Jason Stajich
  • [Bioperl-l] NCBI eutils BioPerl Module   Rob Edwards
  • [Bioperl-l] NCBI eutils BioPerl Module   Allen Day
• [Bioperl-l] Error in bp_genbank2gff3 error   Michael Cipriano
  • [Bioperl-l] Error in bp_genbank2gff3 error   Brian Osborne
• [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Gathman, Allen
  • [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Jason Stajich
• [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Allen Gathman
• [Bioperl-l] Bio::DB::GenPept - get_Seq_by_id   Jamie Sherman
  • [Bioperl-l] Bio::DB::GenPept - get_Seq_by_id   Jason Stajich
• [Bioperl-l] Fetching a DNA sequence corresponding to a protein   Sang Chul Choi
• [Bioperl-l] Problem writing sequence features for GenBank/GenPept sequences (file: Bio/SeqIO/genbank.pm)   sgoegel at gmail.com
  • [Bioperl-l] Problem writing sequence features for GenBank/GenPept sequences (file: Bio/SeqIO/genbank.pm)   Hilmar Lapp
• [Bioperl-l] For a SwissProt protein to get a DNA sequence   Sang Chul Choi
  • [Bioperl-l] For a SwissProt protein to get a DNA sequence   Hilmar Lapp
• [Bioperl-l] dependency XML::DOM::XPath   Hilmar Lapp
• [Bioperl-l] failing tests and dubious warnings   Hilmar Lapp
  • [Bioperl-l] failing tests and dubious warnings   Brian Osborne
    • [Bioperl-l] failing tests and dubious warnings   Jason Stajich
• [Bioperl-l] Re: Bio::OntologyIO choking on current GO   Hilmar Lapp
• [Bioperl-l] Bio::Graphics::Glyph::triangle   Horvath Tamas
• [Bioperl-l] Bio::Graphics::Glyph::triangle   Horvath Tamas
  • [Bioperl-l] Bio::Graphics::Glyph::triangle   Scott Cain
• [Bioperl-l] UniGene   Sean Davis
• [Bioperl-l] possible filehandle out of scope bug between Bio::AlignIO and Bio::Tools::Run::Hmmer   Scott Markel
  • [Bioperl-l] possible filehandle out of scope bug between Bio::AlignIO and Bio::Tools::Run::Hmmer   Jason Stajich
    • [Bioperl-l] possible filehandle out of scope bug between Bio::AlignIO and Bio::Tools::Run::Hmmer   Scott Markel
      • [Bioperl-l] possible filehandle out of scope bug between Bio::AlignIO and Bio::Tools::Run::Hmmer   Jason Stajich
      • [Bioperl-l] possible filehandle out of scope bug between Bio::AlignIO and Bio::Tools::Run::Hmmer   Scott Markel
• [Bioperl-l] UniGene   iluminati at earthlink.net
• [Bioperl-l] Re: BOSC 2005   Darin London
• [Bioperl-l] Bio::Graphics::Glyph::triangle   Scott Cain
• [Bioperl-l] help needed Was:Re: [Gmod-gbrowse] negative numbers in xyplot   Albert Vilella
• [Bioperl-l] Getting Alignment Score from Bio::Tools::Run::Alignment::TCoffee   Edward Wijaya
• [Bioperl-l] Getting Alignment Score from Bio::Tools::Run::Alignment::TCoffee   Edward WIJAYA
• [Bioperl-l] Inconsistency in Alignment Score from Bio::Tools::Run::Alignment::TCoffee versus actual command-line program   Edward WIJAYA
• [Bioperl-l] Re: Bioperl MEME parsing information   Stefan Kirov
  • [Bioperl-l] Re: Bioperl MEME parsing information   Sumit Middha
• [Bioperl-l] Getting Alignment Score from Bio::Tools::Run::Alignment::TCoffee   Jason Stajich
• [Bioperl-l] New Bio::Tools::Spidey::Results module   Ryan Golhar
  • [Bioperl-l] New Bio::Tools::Spidey::Results module   Brian Osborne
• [Bioperl-l] Nearest neighbor from newick format tree   Goel, Manisha
  • [Bioperl-l] Nearest neighbor from newick format tree   Jason Stajich
• [Bioperl-l] Re: Bio::DB::Query   Hilmar Lapp
• [Bioperl-l] Installing BioPerl1.5/DBD/Gbrowse 1.6.2 on MacOSX 10.3.9   David Adelson
  • [Bioperl-l] Installing BioPerl1.5/DBD/Gbrowse 1.6.2 on MacOSX 10.3.9   Jason Stajich
  • [Bioperl-l] Installing BioPerl1.5/DBD/Gbrowse 1.6.2 on MacOSX 10.3.9   Todd Harris
• [Bioperl-l] Bio::Matrix::IO issue   Jon manning
  • [Bioperl-l] Bio::Matrix::IO issue   Jon manning
• [Bioperl-l] Installing BioPerl1.5/DBD/Gbrowse 1.6.2 on MacOSX 10.3.9   David Adelson
  • [Bioperl-l] Installing BioPerl1.5/DBD/Gbrowse 1.6.2 on MacOSX 10.3.9   Sam Kalat
• [Bioperl-l] Re: [Bioperl-guts-l] Re: how to use Storable.pm to save the object?   Jason Stajich
• [Bioperl-l] Temporary name of hmmbuild model   Kary Ann Del Carmen Soriano Ocana
  • [Bioperl-l] Temporary name of hmmbuild model   Jason Stajich
• [Bioperl-l] Cluster::SequenceFamily question   Stefan Kirov
• [Bioperl-l] nested joins   Hilmar Lapp
  • [Bioperl-l] nested joins   Aaron J. Mackey
  • [Bioperl-l] Re: nested joins   Jason Stajich
• [Bioperl-l] survey: perl version   Hilmar Lapp
  • [Bioperl-l] survey: perl version   Scott Cain
• [Bioperl-l] Entrez Gene solution : code available   Mark Lambrecht
• [Bioperl-l] survey: perl version   Pinglei Zhou
• [Bioperl-l] survey: perl version   Susan Russo
• [Bioperl-l] Re: How to extend a class in bioperl?   Jason Stajich
• [Bioperl-l] Re: How to extend a class in bioperl?   Jason Stajich
• [Bioperl-l] Fwd: [Bioperl-guts-l] AffyDB a module to handle Affymetrix annotation tables and more...   Jason Stajich
• [Bioperl-l] retrieving sequences by ID   sokeeff at tcd.ie
  • [Bioperl-l] retrieving sequences by ID   Devin Scannell
• [Bioperl-l] updates, new code, invitation to contribute   Jason Stajich
  • [Bioperl-l] Mapping Coordinates   Navin Elango
  • [Bioperl-l] updates, new code, invitation to contribute   Hilmar Lapp
    • [Bioperl-l] updates, new code, invitation to contribute   Terry Jones
    • [Bioperl-l] updates, new code, invitation to contribute   James Wasmuth
    • [Bioperl-l] updates, new code, invitation to contribute   Allen Day
  • [Bioperl-l] updates, new code, invitation to contribute   Nathan Haigh
• [Bioperl-l] RE: Installing BioPerl on Windows   Brian Osborne
• [Bioperl-l] Bioperl on Mac OS X   Koen van der Drift
• [Bioperl-l] How to specify alignment view in RemoteBlast   Paul Cantalupo
• [Bioperl-l] retrieving sequences by ID   Sean O'Keeffe
  • [Bioperl-l] retrieving sequences by ID   Raoul Jean Pierre Bonnal
  • [Bioperl-l] retrieving sequences by ID   Diego Riano
  • [Bioperl-l] retrieving sequences by ID   khoueiry
  • [Bioperl-l] retrieving sequences by ID   Jason Stajich
  • [Bioperl-l] retrieving sequences by ID   Brian Osborne
• [Bioperl-l] Protdist output to generic matrix   Goel, Manisha
  • [Bioperl-l] Protdist output to generic matrix   Jason Stajich
• [Bioperl-l] Bio::Ontology::Term references quetsion   Stefan Kirov
  • [Bioperl-l] Bio::Ontology::Term references quetsion   Hilmar Lapp
    • [Bioperl-l] Bio::Ontology::Term references quetsion   Stefan Kirov
• [Bioperl-l] Having no luck installing bioperl in Fedora Core 3 with Perl 5.8.5   Oliver Homann
  • [Bioperl-l] Having no luck installing bioperl in Fedora Core 3 with Perl 5.8.5   Scott Cain
    • [Bioperl-l] Trouble with fetching a sequence from indexed fasta file   Oliver Homann
      • [Bioperl-l] Trouble with fetching a sequence from indexed fasta file   Andrew Walsh
  • [Bioperl-l] Having no luck installing bioperl in Fedora Core 3 with Perl 5.8.5   Stefan Kirov
• [Bioperl-l] different label colours   Horvath Tamas
• [Bioperl-l] Trouble with fetching a sequence from indexed fasta file   Crabtree, Jonathan
• [Bioperl-l] different label colours   Crabtree, Jonathan
  • [Bioperl-l] different label colours   Horvath Tamas
• [Bioperl-l] BLAST results format   Nathan Haigh
• [Bioperl-l] Windows BLAST problems under Cygwin   Paul Cantalupo
  • [Bioperl-l] Windows BLAST problems under Cygwin   Jason Stajich
    • [Bioperl-l] Windows BLAST problems under Cygwin   Brian Osborne
      • [Bioperl-l] Windows BLAST problems under Cygwin   Paul G Cantalupo
• [Bioperl-l] different label colours   Crabtree, Jonathan
  • [Bioperl-l] different label colours   Horvath Tamas
• [Bioperl-l] different label colours   Crabtree, Jonathan
  • [Bioperl-l] different label colours   Horvath Tamas
• [Bioperl-l] different label colours   Crabtree, Jonathan
• [Bioperl-l] Format of BlastHit '_description' key   Paul G Cantalupo
• [Bioperl-l] RemoteBlast - hit table and html format   Madeleine Lemieux

Last message date: Fri Apr 29 15:44:41 EST 2005
Archived on: Sat Apr 30 12:25:43 EST 2005

• Messages sorted by: [ subject ] [ author ] [ date ]
• More info on this list...