lang.perl.bio.general (date)

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lang.perl.bio.general (date)

November 30, 2003

Mobiform SVG Browser and SVGViewPlus for .NET, info

November 28, 2003

Re: Small Bio::Factory::EMBOSS typo, Heikki Lehvaslaiho
ProServer, a pluggable DAS server, Bio::SeqIO support added, Andreas Kahari
CONGRATULATIONS YOU HAVE WON, Lotto International

November 27, 2003

Re: Bio::SeqIO Genbank + EMBL unquoted values, Heikki Lehvaslaiho
Re: newick to nexus, Jason Stajich
Re: newick to nexus, Shawn Hoon
Re: newick to nexus, Rob Edwards
newick to nexus, Lewis Lukens
Bio::SeqIO Genbank + EMBL unquoted values, Nadeem Faruque

November 26, 2003

Re: [BioPerl] Re: Bio::Perl blast function not working?, Mark Wilkinson
Re: [BioPerl] Re: Bio::Perl blast function not working?, Heikki Lehvaslaiho
about the Bio::SeqIO::staden::read, Magic Fang
Re: AUTHORS reference field in genbank file?, Joshua A Udall
Re: AUTHORS reference field in genbank file?, Jason Stajich
AUTHORS reference field in genbank file?, Wes Barris

November 25, 2003

Re: [BioPerl] Re: Bio::Perl blast function not working?, Mark Wilkinson
Re: Developers: what do you want to fix before 1.4 release?, Heikki Lehvaslaiho
Bio::Restriction issues, Heikki Lehvaslaiho
Re: Developers: what do you want to fix before 1.4 release?, Jason Stajich
Re: [BioPerl] Re: Bio::Perl blast function not working?, Jason Stajich
Re: [BioPerl] Re: Bio::Perl blast function not working, paul . boutros
Re: [BioPerl] Re: Bio::Perl blast function not working?, Rob Edwards
Re: [BioPerl] Re: Bio::Perl blast function not working?, Mark Wilkinson
Re: Developers: what do you want to fix before 1.4 release?, Heikki Lehvaslaiho
Re: Bio::Perl blast function not working?, Jason Stajich
Bio::Perl blast function not working?, Mark Wilkinson
Re: Re: Developers: what do you want to fix before 1.4 release?, Stefan Kirov
Re: why i can not find Bio::SeqIO::staden::read in bioperl-ext packages, Jason Stajich
why i can not find Bio::SeqIO::staden::read in bioperl-ext packages, Magic Fang
Re: Developers: what do you want to fix before 1.4 release?, Steve Chervitz

November 24, 2003

Re: Re: Developers: what do you want to fix before 1.4 release?, Heikki Lehvaslaiho
Re: Developers: what do you want to fix before 1.4 release?, Jason Stajich
Re: [Bioperl-announce-l] Bioperl Developer snapshot 1.3.03, Steve Chervitz
Re: How to distinguish pdb Helix from Sheet?, Jason Stajich
Re: Developers: what do you want to fix before 1.4 release?, Todd Harris
Re: Problems with SearchIO and SearchIO::HTMLResultwriter, Jason Stajich
RE: Problems with SearchIO and SearchIO::HTMLResultwr iter, michael watson (IAH-C)
Re: GD/SVG (was: new to the group), Ronan Oger
Problems with SearchIO and SearchIO::HTMLResultwriter, michael watson (IAH-C)
Re: Graphics:Panel /SeqFeature::Generic, Daniel Lang
Re: Graphics:Panel /SeqFeature::Generic, Daniel Lang
Developers: what do you want to fix before 1.4 release?, Heikki Lehvaslaiho
Re: GD/SVG (was: new to the group), Todd Harris
Re: GFF file output missing semicolon, Wes Barris
Re: GFF file output missing semicolon, Wes Barris
Re: STDERR?, Wes Barris

November 23, 2003

STDERR?, Vesko Baev

November 22, 2003

Re: How can i get tag Comments from Genbank file, Jason Stajich
How to distinguish pdb Helix from Sheet?, Jeff Donner
How can i get tag Comments from Genbank file, Fabiola Sánchez

November 21, 2003

Re: GFF file output missing semicolon, Jason Stajich
Re: GFF file output missing semicolon, Lincoln Stein
Re: Re: bioperl Registry, Heikki Lehvaslaiho
Re: MS: Calculation of theoretical spectra, Jonathan Epstein
Bioperl Developer snapshot 1.3.03, Heikki Lehvaslaiho
Re: Re: bioperl Registry, Lincoln Stein
Still working with biopipe...., matthieu CONTE
[Bioperl-] Alignment Score for ClustalW using the factory, Iain Wallace
MS: Calculation of theoretical spectra, Andreas Boehm
Re: Re: bioperl Registry, Heikki Lehvaslaiho
Re: Re: bioperl Registry, Lincoln Stein
Re: Re: bioperl Registry, Heikki Lehvaslaiho
Re: Searching the bioperl archive, Jason Stajich
GFF file output missing semicolon, Wes Barris
Re: bioperl Registry, Lincoln Stein
Searching the bioperl archive, Andy Hammer
Re: Drawing Chromosomes, Lincoln Stein
Re: proposed additions to SeqFeatureI, RangeI and FeatureHolderI, Lincoln Stein

November 20, 2003

Re: Drawing chromosomes in Generic Genome Browser, Lincoln Stein
AcePerl Makefile problem w perl 5.8.0, Philip MacMenamin
Re: Capabilities of Bio::Tree, Jason Stajich
Total OBF server shutdown Saturday November 22nd (all day EDT timezone), Chris Dagdigian
Drawing Chromosomes, Gaetan
Drawing chromosomes in Generic Genome Browser, Gaetan
Capabilities of Bio::Tree, Bryony Mackenzie
RE: Newbie question: Removing sequences from alignment, Brian Osborne
Newbie question: Removing sequences from alignment, Iain Wallace
Blast, Richard Adams
Re: usage of Bio::SeqIO::tigr, Josh Lauricha
proposed additions to SeqFeatureI, RangeI and FeatureHolderI, Chris Mungall
Re: usage of Bio::SeqIO::tigr, Jason Stajich

November 19, 2003

usage of Bio::SeqIO::tigr, Yue Ke
usage of Bio::SeqIO::tigr, Yue Ke
usage of Bio::SeqIO::tigr, Yue Ke
Re: new to the group. And a quick demo of SVG::GD, Ronan Oger
Bio::Tools::Phylo::Phylip::ProtDist module: warning message for bootstrapped data file, Jack Chen
Re: [Bioperl-pipeline] need help with biopipe, Shawn Hoon

November 18, 2003

Re: Graphics:Panel /SeqFeature::Generic, Lincoln Stein
Re: new to the group. And a quick demo of SVG::GD, Todd Harris
need help with biopipe, matthieu CONTE
RE: RE: about pdb parsing, Jurgen Pletinckx
RE: about pdb parsing, Jurgen Pletinckx
location of non-bioperl code in the Bio:: tree, Reece Hart

November 17, 2003

Graphics:Panel /SeqFeature::Generic, Daniel Lang
Blast, Guido Dieterich

November 16, 2003

Re: PCR, Rob Edwards
Re: PCR, Heikki Lehvaslaiho
PCR, Vesko Baev

November 14, 2003

Re: new to the group. And a quick demo of SVG::GD, Lincoln Stein
Re: Problem or Bug with Bio::, Jason Stajich
Problem or Bug with Bio::LocatableSeq, hyupaik
Problem or Bug with Bio::, hyupaik
RE: Problem with Bio::SeqIO opening gzipped files, Jason Stajich
RE: Problem with Bio::SeqIO opening gzipped files, Brian Osborne
Codeml.pm/PAML.pm, Derek Gatherer
Re: Problem with Bio::SeqIO opening gzipped files, Jason Stajich
new HOWTO: SimpleWebAnalysis, Heikki Lehvaslaiho
Re: Problem with Bio::SeqIO opening gzipped files, Zayed Albertyn
Re: Problem with Bio::SeqIO opening gzipped files, Andreas Kahari
Re: Problem with Bio::SeqIO opening gzipped files, Zayed Albertyn
Re: Problem with Bio::SeqIO opening gzipped files, Andreas Kahari
Re: Problem with Bio::SeqIO opening gzipped files, Zayed Albertyn
Re: Problem with Bio::SeqIO opening gzipped files, Zayed Albertyn
Re: Problem with Bio::SeqIO opening gzipped files, Andreas Kahari
Problem with Bio::SeqIO opening gzipped files, Zayed Albertyn

November 13, 2003

Re: standaloneblast executable location?, Jason Stajich
standaloneblast executable location?, Wes Barris
new to the group. And a quick demo of SVG::GD, Ronan Oger
Re: tests failing, please help, Stefan Kirov
Re: tests failing, please help, Lincoln Stein
SeqFeature test, Stefan Kirov
Re: xyplot weirdness, Lincoln Stein
RE: tests failing, please help, Brian Osborne
Re: Bio::AlignIO::po, Jason Stajich
RE: Bio::Tools::Run::StandAloneBlast, Jason Stajich
Bio::AlignIO::po, Matthew Betts
xyplot weirdness, Tobias
RE: Bio::Tools::Run::StandAloneBlast, Mehta, Perdeep
tests failing, please help, Heikki Lehvaslaiho
Re: Bio::Tools::Run::StandAloneBlast, Wes Barris
RE: Bio::Tools::Run::StandAloneBlast, Mehta, Perdeep
Re: Bio::Tools::Run::StandAloneBlast, Jason Stajich

November 12, 2003

Bio::Tools::Run::StandAloneBlast, Mehta, Perdeep
Join Our Studies! Current Study (Molecular Testing Professionals), Pat Jones
Re: Drawing Chromosomes, Lincoln Stein
Re: which GD.pm for libgd1.so.1.8.4, Lincoln Stein
Re: about the GD problem, Lincoln Stein
Re: passing $result, Jason Stajich
Drawing Chromosomes, Johnny Amos
Re: passing $result, Andreas Kahari
passing $result, Joshua A Udall
Re: about the FgeneSH parser, Magic Fang
about the GD problem, Magic Fang

November 11, 2003

which GD.pm for libgd1.so.1.8.4, Charles Hauser
Re: SiteMatrix, Stefan Kirov
SiteMatrix, Stefan Kirov
SiteMatrix, Heikki Lehvaslaiho
Re: [Bioperl-guts-l] bioperl-live SeqFeature test hanging, Heikki Lehvaslaiho

November 10, 2003

Re: [Gmod-schema] load_gff3 handles ##sequence-region, Scott Cain
Re: Bio::Tools::Run::Phylo::PAML::Codeml, Jason Stajich
Re: Bio::Tools::Run::Phylo::PAML::Codeml, Heikki Lehvaslaiho
Re: SeqWords.pm, Heikki Lehvaslaiho
Bio::Tools::Run::Phylo::PAML::Codeml, Derek Gatherer
Re: about the FgeneSH parser, Todd Harris
SeqWords.pm, Derek Gatherer
Re: Bio::AlignIO::bl2seq doesn't know when to stop..., Jonathan Manning
Re: about the FgeneSH parser, Magic Fang
Re: about the FgeneSH parser, Heikki Lehvaslaiho
RE: How to check the validity of an accession number ?, michael watson (IAH-C)
about the FgeneSH parser, Magic Fang
Re: SeqFeatureI::display_name, Hilmar Lapp
Score computation in psl.pm, Wes Barris

November 09, 2003

Re: bioperl meme/mast parser?, Stefan A Kirov
bioperl meme/mast parser?, Alok Saldanha
(no subject), Sanjib Dutta
Re: How to check the validity of an accession number ?, Heikki Lehvaslaiho
Re: How to check the validity of an accession number ?, Damien Marsic
Re: suggestion for drawing pedigrees, Jason Stajich
Re: [BioPerl] Re: How to check the validity of an accession number ?, Jason Stajich
Re: How to check the validity of an accession number ?, Damien Marsic

November 08, 2003

Re: [BioPerl] Re: How to check the validity of an accession number ?, Mark Wilkinson
Re: [BioPerl] Re: How to check the validity of an accession number ?, Heikki Lehvaslaiho
Re: embl.pm and virus names, Heikki Lehvaslaiho
Re: problems with Bio::Tools::GFF, Lincoln Stein
Re: [BioPerl] Re: How to check the validity of an accession number ?, Mark Wilkinson
Re: Understanding LocatableSeq, Heikki Lehvaslaiho
Re: How to check the validity of an accession number ?, Heikki Lehvaslaiho
How to check the validity of an accession number ?, Damien Marsic
load_gff3 handles ##sequence-region, Allen Day

November 07, 2003

suggestion for drawing pedigrees, Lowell Umayam
Re: psl to gff?, Jason Stajich
Re: macperl, Todd Richmond
psl to gff?, Wes Barris
Re: Understanding LocatableSeq, Wes Barris
Re: macperl, Hilmar Lapp
macperl, Liam Elbourne

November 06, 2003

Re: [BioSQL-l] (no subject), Hilmar Lapp
embl.pm and virus names, Neil Rawlings
BioSQL, matthieu CONTE

November 05, 2003

Enabling SVG output from Bio::Graphics, Todd Harris
Re: Bio::Tools::FootPrinter, Shawn Hoon
Re: Bio::Graphics::Feature, Lincoln Stein
RE: Concatenating Bacterial Genome Sequence, Lin, Xiaoying
Re: Re: problems with Bio::Tools::GFF, Lincoln Stein
Re: Fwd: Re: haplotype, Jason Stajich
Fwd: Re: haplotype, Pedro
Concatenating Bacterial Genome Sequence, michael watson (IAH-C)
Re: haplotype, Ewan Birney
haplotype, Pedro
Bio::Graphics::Feature, Jason Stajich
Bio::Tools::FootPrinter, ypeng

November 04, 2003

Re: RPSblast and existing BLAST packages (WAS: RemoteBlast), Richard Adams
Bio::AlignIO::bl2seq doesn't know when to stop..., Jonathan M. Manning
RE: [Gmod-gbrowse] gbrowse: creating link based on 'Note' feature, Marc Logghe
gbrowse: creating link based on 'Note' feature, Charles Hauser
Re: RPSblast and existing BLAST packages (WAS: RemoteBlast), Will Spooner
RepeatMasker, Crook, R.
RPSblast and existing BLAST packages (WAS: RemoteBlast), Richard Adams
Re: Understanding LocatableSeq, Ewan Birney
Re: how to set first line of genbank file, Hilmar Lapp
Re: OMIM tests failing, Hilmar Lapp
Re: OMIM tests failing, Juguang Xiao
Re: Understanding LocatableSeq, Jason Stajich
Re: post translational modifications, Jason Stajich
Re: Understanding LocatableSeq, Wes Barris
post translational modifications, Koen van der Drift

November 03, 2003

Re: Understanding LocatableSeq, Ewan Birney
Understanding LocatableSeq, Wes Barris
Re: Bio::Tools::Run::Alignment::Clustalw, Josh Lauricha
Bio::Tools::Run::Alignment::Clustalw, Josh Lauricha
Re: get_sequence error retrieving protein sequences from GenBank, Jason Stajich
Re: Bio::SeqIO::tigr, Josh Lauricha
get_sequence error retrieving protein sequences from GenBank, Warren Alden Kibbe
Re: Bio::SeqIO::tigr, Jason Stajich
Re: how to set first line of genbank file, Jason Stajich
Re: Bio::SeqIO::tigr, Josh Lauricha
Re: problems with Bio::Tools::GFF, Jason Stajich
Re: problems with Bio::Tools::GFF, Scott Cain
Re: problems with Bio::Tools::GFF, Jason Stajich
Re: bioperl and Bio::Factory::EMBOSS via cgi...permissionproblems?, Tobias
SeqFeatureI->spliced_translation, Matthew Betts
problems with Bio::Tools::GFF, Scott Cain
RE: (no subject), Brian Osborne
(no subject), Nokes, Rebecca (BearingPoint)
Re: Bio::SeqIO::tigr, Aaron J.Mackey
Re: Bio::SeqIO::tigr, Jason Stajich
Re: bioperl and Bio::Factory::EMBOSS via cgi... permission problems?, Rob Edwards
gcg.pm, another comment, Derek Gatherer
RE: bioperl and Bio::Factory::EMBOSS via cgi... permissionproblems?, Brian Osborne
RE: how to tun bioperl and parsing blast report, Brian Osborne
bioperl and Bio::Factory::EMBOSS via cgi... permission problems?, Tobias
RPSblast and existing BLAST packages (WAS: RemoteBlast), Donald G. Jackson
how to tun bioperl and parsing blast report, hank wong
Help with testing of parallel Smith-Waterman code on x86 workstations, Iain Wallace
RE: Glimmer, Jason Stajich
Re: help with BLAST, Remo Sanges
RE: Glimmer, michael watson (IAH-C)
RE: Glimmer, Jason Stajich
RE: Glimmer, michael watson (IAH-C)
help with BLAST, Crook, R.
how to set first line of genbank file, Magic Fang
Re: OMIM tests failing, Hilmar Lapp

November 01, 2003

OMIM tests failing, Allen Day

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