lang.perl.bio.general (thread)

Mobiform SVG Browser and SVGViewPlus for .NET, info
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
newick to nexus, Lewis Lukens
- Re: newick to nexus, Rob Edwards
- Re: newick to nexus, Shawn Hoon
- Re: newick to nexus, Jason Stajich
Bio::SeqIO Genbank + EMBL unquoted values, Nadeem Faruque
- Re: Bio::SeqIO Genbank + EMBL unquoted values, Heikki Lehvaslaiho
about the Bio::SeqIO::staden::read, Magic Fang
AUTHORS reference field in genbank file?, Wes Barris
- Re: AUTHORS reference field in genbank file?, Jason Stajich
- Re: AUTHORS reference field in genbank file?, Joshua A Udall
Bio::Restriction issues, Heikki Lehvaslaiho
Re: [BioPerl] Re: Bio::Perl blast function not working, paul . boutros
Bio::Perl blast function not working?, Mark Wilkinson
- Re: Bio::Perl blast function not working?, Jason Stajich
  - Re: [BioPerl] Re: Bio::Perl blast function not working?, Mark Wilkinson
    - Re: [BioPerl] Re: Bio::Perl blast function not working?, Rob Edwards
    - Re: [BioPerl] Re: Bio::Perl blast function not working?, Jason Stajich
    - Re: [BioPerl] Re: Bio::Perl blast function not working?, Mark Wilkinson
    - Re: [BioPerl] Re: Bio::Perl blast function not working?, Heikki Lehvaslaiho
    - Re: [BioPerl] Re: Bio::Perl blast function not working?, Mark Wilkinson
why i can not find Bio::SeqIO::staden::read in bioperl-ext packages, Magic Fang
- Re: why i can not find Bio::SeqIO::staden::read in bioperl-ext packages, Jason Stajich
Re: Developers: what do you want to fix before 1.4 release?, Todd Harris
- Re: Re: Developers: what do you want to fix before 1.4 release?, Heikki Lehvaslaiho
  - Re: Re: Developers: what do you want to fix before 1.4 release?, Stefan Kirov
RE: Problems with SearchIO and SearchIO::HTMLResultwr iter, michael watson (IAH-C)
Problems with SearchIO and SearchIO::HTMLResultwriter, michael watson (IAH-C)
- Re: Problems with SearchIO and SearchIO::HTMLResultwriter, Jason Stajich
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: Developers: what do you want to fix before 1.4 release?, Steve Chervitz
    - 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: Developers: what do you want to fix before 1.4 release?, Heikki Lehvaslaiho
STDERR?, Vesko Baev
- Re: STDERR?, Wes Barris
How to distinguish pdb Helix from Sheet?, Jeff Donner
- Re: How to distinguish pdb Helix from Sheet?, Jason Stajich
How can i get tag Comments from Genbank file, Fabiola Sánchez
- Re: How can i get tag Comments from Genbank file, Jason Stajich
Bioperl Developer snapshot 1.3.03, Heikki Lehvaslaiho
- Re: [Bioperl-announce-l] Bioperl Developer snapshot 1.3.03, Steve Chervitz
Still working with biopipe...., matthieu CONTE
[Bioperl-] Alignment Score for ClustalW using the factory, Iain Wallace
MS: Calculation of theoretical spectra, Andreas Boehm
- Re: MS: Calculation of theoretical spectra, Jonathan Epstein
GFF file output missing semicolon, Wes Barris
- Re: GFF file output missing semicolon, Lincoln Stein
  - Re: GFF file output missing semicolon, Jason Stajich
    - Re: GFF file output missing semicolon, Wes Barris
  - Re: GFF file output missing semicolon, Wes Barris
Re: bioperl Registry, Lincoln Stein
- Re: Re: bioperl Registry, Heikki Lehvaslaiho
  - Re: Re: bioperl Registry, Lincoln Stein
    - Re: Re: bioperl Registry, Heikki Lehvaslaiho
    - Re: Re: bioperl Registry, Lincoln Stein
    - Re: Re: bioperl Registry, Heikki Lehvaslaiho
Searching the bioperl archive, Andy Hammer
- Re: Searching the bioperl archive, Jason Stajich
AcePerl Makefile problem w perl 5.8.0, Philip MacMenamin
Total OBF server shutdown Saturday November 22nd (all day EDT timezone), Chris Dagdigian
Drawing chromosomes in Generic Genome Browser, Gaetan
- Re: Drawing chromosomes in Generic Genome Browser, Lincoln Stein
Capabilities of Bio::Tree, Bryony Mackenzie
- Re: Capabilities of Bio::Tree, Jason Stajich
Newbie question: Removing sequences from alignment, Iain Wallace
- RE: Newbie question: Removing sequences from alignment, Brian Osborne
proposed additions to SeqFeatureI, RangeI and FeatureHolderI, Chris Mungall
- Re: proposed additions to SeqFeatureI, RangeI and FeatureHolderI, Lincoln Stein
usage of Bio::SeqIO::tigr, Yue Ke
- usage of Bio::SeqIO::tigr, Yue Ke
- usage of Bio::SeqIO::tigr, Yue Ke
  - Re: usage of Bio::SeqIO::tigr, Jason Stajich
    - Re: usage of Bio::SeqIO::tigr, Josh Lauricha
need help with biopipe, matthieu CONTE
- Re: [Bioperl-pipeline] need help with biopipe, Shawn Hoon
  - Bio::Tools::Phylo::Phylip::ProtDist module: warning message for bootstrapped data file, Jack Chen
RE: about pdb parsing, Jurgen Pletinckx
- RE: RE: about pdb parsing, Jurgen Pletinckx
location of non-bioperl code in the Bio:: tree, Reece Hart
Graphics:Panel /SeqFeature::Generic, Daniel Lang
- Re: Graphics:Panel /SeqFeature::Generic, Lincoln Stein
  - Re: Graphics:Panel /SeqFeature::Generic, Daniel Lang
  - Re: Graphics:Panel /SeqFeature::Generic, Daniel Lang
Blast, Guido Dieterich
- Blast, Richard Adams
PCR, Vesko Baev
- Re: PCR, Heikki Lehvaslaiho
- Re: PCR, Rob Edwards
new HOWTO: SimpleWebAnalysis, Heikki Lehvaslaiho
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
    - 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, Jason Stajich
    - RE: Problem with Bio::SeqIO opening gzipped files, Brian Osborne
    - RE: Problem with Bio::SeqIO opening gzipped files, Jason Stajich
    - Problem or Bug with Bio::, hyupaik
    - Re: Problem or Bug with Bio::, Jason Stajich
    - Problem or Bug with Bio::LocatableSeq, hyupaik
standaloneblast executable location?, Wes Barris
- Re: standaloneblast executable location?, Jason Stajich
new to the group. And a quick demo of SVG::GD, Ronan Oger
- Re: new to the group. And a quick demo of SVG::GD, Lincoln Stein
- Re: new to the group. And a quick demo of SVG::GD, Todd Harris
  - Re: new to the group. And a quick demo of SVG::GD, Ronan Oger
    - Re: GD/SVG (was: new to the group), Todd Harris
    - Re: GD/SVG (was: new to the group), Ronan Oger
SeqFeature test, Stefan Kirov
Bio::AlignIO::po, Matthew Betts
- Re: Bio::AlignIO::po, Jason Stajich
xyplot weirdness, Tobias
- Re: xyplot weirdness, Lincoln Stein
tests failing, please help, Heikki Lehvaslaiho
- RE: tests failing, please help, Brian Osborne
- Re: tests failing, please help, Lincoln Stein
- Re: tests failing, please help, Stefan Kirov
Bio::Tools::Run::StandAloneBlast, Mehta, Perdeep
- Re: Bio::Tools::Run::StandAloneBlast, Jason Stajich
- RE: Bio::Tools::Run::StandAloneBlast, Mehta, Perdeep
  - Re: Bio::Tools::Run::StandAloneBlast, Wes Barris
- RE: Bio::Tools::Run::StandAloneBlast, Mehta, Perdeep
  - RE: Bio::Tools::Run::StandAloneBlast, Jason Stajich
Join Our Studies! Current Study (Molecular Testing Professionals), Pat Jones
Drawing Chromosomes, Johnny Amos
- Re: Drawing Chromosomes, Lincoln Stein
- Drawing Chromosomes, Gaetan
  - Re: Drawing Chromosomes, Lincoln Stein
passing $result, Joshua A Udall
- Re: passing $result, Andreas Kahari
- Re: passing $result, Jason Stajich
about the GD problem, Magic Fang
- Re: about the GD problem, Lincoln Stein
which GD.pm for libgd1.so.1.8.4, Charles Hauser
- Re: which GD.pm for libgd1.so.1.8.4, Lincoln Stein
SiteMatrix, Heikki Lehvaslaiho
- Message not available
  - Message not available
    - Re: SiteMatrix, Stefan Kirov
- SiteMatrix, Stefan Kirov
Re: [Bioperl-guts-l] bioperl-live SeqFeature test hanging, Heikki Lehvaslaiho
Bio::Tools::Run::Phylo::PAML::Codeml, Derek Gatherer
- Re: Bio::Tools::Run::Phylo::PAML::Codeml, Heikki Lehvaslaiho
- Re: Bio::Tools::Run::Phylo::PAML::Codeml, Jason Stajich
SeqWords.pm, Derek Gatherer
- Re: SeqWords.pm, Heikki Lehvaslaiho
  - Codeml.pm/PAML.pm, Derek Gatherer
RE: How to check the validity of an accession number ?, michael watson (IAH-C)
about the FgeneSH parser, Magic Fang
- Re: about the FgeneSH parser, Heikki Lehvaslaiho
  - Re: about the FgeneSH parser, Magic Fang
  - Re: about the FgeneSH parser, Todd Harris
    - Re: about the FgeneSH parser, Magic Fang
Re: SeqFeatureI::display_name, Hilmar Lapp
Score computation in psl.pm, Wes Barris
bioperl meme/mast parser?, Alok Saldanha
- Re: bioperl meme/mast parser?, Stefan A Kirov
How to check the validity of an accession number ?, Damien Marsic
- Re: How to check the validity of an accession number ?, Heikki Lehvaslaiho
  - 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: [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 ?, Jason Stajich
  - Re: How to check the validity of an accession number ?, Damien Marsic
    - Re: How to check the validity of an accession number ?, Damien Marsic
    - Re: How to check the validity of an accession number ?, Heikki Lehvaslaiho
load_gff3 handles ##sequence-region, Allen Day
- Re: [Gmod-schema] load_gff3 handles ##sequence-region, Scott Cain
suggestion for drawing pedigrees, Lowell Umayam
- Re: suggestion for drawing pedigrees, Jason Stajich
psl to gff?, Wes Barris
- Re: psl to gff?, Jason Stajich
macperl, Liam Elbourne
- Re: macperl, Hilmar Lapp
- Re: macperl, Todd Richmond
Re: [BioSQL-l] (no subject), Hilmar Lapp
embl.pm and virus names, Neil Rawlings
- Re: embl.pm and virus names, Heikki Lehvaslaiho
BioSQL, matthieu CONTE
Enabling SVG output from Bio::Graphics, Todd Harris
Concatenating Bacterial Genome Sequence, michael watson (IAH-C)
- RE: Concatenating Bacterial Genome Sequence, Lin, Xiaoying
haplotype, Pedro
- Re: haplotype, Ewan Birney
- Fwd: Re: haplotype, Pedro
  - Re: Fwd: Re: haplotype, Jason Stajich
Bio::Graphics::Feature, Jason Stajich
- Re: Bio::Graphics::Feature, Lincoln Stein
Bio::Tools::FootPrinter, ypeng
- Re: Bio::Tools::FootPrinter, Shawn Hoon
Bio::AlignIO::bl2seq doesn't know when to stop..., Jonathan M. Manning
- Re: Bio::AlignIO::bl2seq doesn't know when to stop..., Jonathan Manning
RE: [Gmod-gbrowse] gbrowse: creating link based on 'Note' feature, Marc Logghe
gbrowse: creating link based on 'Note' feature, Charles Hauser
RepeatMasker, Crook, R.
post translational modifications, Koen van der Drift
- Re: post translational modifications, Jason Stajich
Understanding LocatableSeq, Wes Barris
- Re: Understanding LocatableSeq, Ewan Birney
  - Re: Understanding LocatableSeq, Wes Barris
    - Re: Understanding LocatableSeq, Jason Stajich
    - Re: Understanding LocatableSeq, Wes Barris
    - Re: Understanding LocatableSeq, Heikki Lehvaslaiho
    - Re: Understanding LocatableSeq, Ewan Birney
Bio::Tools::Run::Alignment::Clustalw, Josh Lauricha
- Re: Bio::Tools::Run::Alignment::Clustalw, Josh Lauricha
get_sequence error retrieving protein sequences from GenBank, Warren Alden Kibbe
- Re: get_sequence error retrieving protein sequences from GenBank, Jason Stajich
SeqFeatureI->spliced_translation, Matthew Betts
problems with Bio::Tools::GFF, Scott Cain
- 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: Re: problems with Bio::Tools::GFF, Lincoln Stein
- Re: problems with Bio::Tools::GFF, Lincoln Stein
(no subject), Nokes, Rebecca (BearingPoint)
- RE: (no subject), Brian Osborne
- (no subject), Sanjib Dutta
Re: Bio::SeqIO::tigr, Jason Stajich
- Re: Bio::SeqIO::tigr, Aaron J.Mackey
  - Re: Bio::SeqIO::tigr, Josh Lauricha
- Re: Bio::SeqIO::tigr, Josh Lauricha
  - Re: Bio::SeqIO::tigr, Jason Stajich
gcg.pm, another comment, Derek Gatherer
bioperl and Bio::Factory::EMBOSS via cgi... permission problems?, Tobias
- RE: bioperl and Bio::Factory::EMBOSS via cgi... permissionproblems?, Brian Osborne
  - Re: bioperl and Bio::Factory::EMBOSS via cgi...permissionproblems?, Tobias
- Re: bioperl and Bio::Factory::EMBOSS via cgi... permission problems?, Rob Edwards
RPSblast and existing BLAST packages (WAS: RemoteBlast), Donald G. Jackson
- RPSblast and existing BLAST packages (WAS: RemoteBlast), Richard Adams
  - Re: RPSblast and existing BLAST packages (WAS: RemoteBlast), Will Spooner
    - Re: RPSblast and existing BLAST packages (WAS: RemoteBlast), Richard Adams
how to tun bioperl and parsing blast report, hank wong
- RE: how to tun bioperl and parsing blast report, Brian Osborne
Help with testing of parallel Smith-Waterman code on x86 workstations, Iain Wallace
RE: Glimmer, michael watson (IAH-C)
- RE: Glimmer, Jason Stajich
- RE: Glimmer, michael watson (IAH-C)
  - RE: Glimmer, Jason Stajich
help with BLAST, Crook, R.
- Re: help with BLAST, Remo Sanges
how to set first line of genbank file, Magic Fang
- Re: how to set first line of genbank file, Jason Stajich
  - Re: how to set first line of genbank file, Hilmar Lapp
OMIM tests failing, Allen Day
- Re: OMIM tests failing, Hilmar Lapp
  - Re: OMIM tests failing, Juguang Xiao
    - Re: OMIM tests failing, Hilmar Lapp