lang.perl.bio.general (date)

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lang.perl.bio.general (date)

July 31, 2003

Re: $_ assignment question, Josh Lauricha
Re: distant thoughts from a dinosaur..., Paul Edlefsen
Re: $_ assignment question, Paul Edlefsen
Re: $_ assignment question, Josh Lauricha
Re: $_ assignment question, Aaron J Mackey
RE: List archives now searchable; feedback needed, Brian Osborne
Re: $_ assignment question, Hilmar Lapp
Re: multiple inheritance, Hilmar Lapp
Re: $_ assignment question, Jason Stajich
Re: $_ assignment question, Hilmar Lapp
Re: multiple inheritance, Nathan \(Nat\) Goodman
blastcl3, Jennifer Thornton
blastcl3, Nini1078
Re: multiple inheritance, Matthew Pocock
Re: Re: [Gmod-schema] Re: BioSQL or chado, Hilmar Lapp
RE: multiple inheritance, Christopher Cavnor
Re: $_ assignment question, Jonathan Barber
Re: $_ assignment question, Jason Stajich
Re: secondary structure: AlignI ?, Jason Stajich
Re: Parsing a netblast file, Jason Stajich
$_ assignment question, Jonathan Barber
secondary structure: AlignI ?, Allen Day
Re: multiple inheritance, Ewan Birney
ps_scan parser and runner, Juguang Xiao
Panel add_track -label option does not work, Wes Barris
Parsing a netblast file, Wes Barris

July 30, 2003

Re: how versions work in bioperl, Philip MacMenamin
how versions work in bioperl, Jason Stajich
RE: multiple inheritance, Nathan \(Nat\) Goodman
Re: multiple inheritance, Steve Mathias
Re: No version numbers on bioperl pms., Philip MacMenamin
multiple inheritance, Jason Stajich
Re: No version numbers on bioperl pms., Jason Stajich
Re: No version numbers on bioperl pms., Philip MacMenamin
failing tests, Hilmar Lapp
Re: Re: BioSQL or chado, Hilmar Lapp
Re: [Gmod-schema] Re: BioSQL or chado, Allen Day
Re: [Gmod-schema] Re: BioSQL or chado, Chris Mungall
Re: filtering output from HTMLResultWriter, Charles Hauser
Re: No version numbers on bioperl pms., Jason Stajich
No version numbers on bioperl pms., philip
Re: BioSQL or chado, Andrew Nunberg
RE: Bioperl install tests behind firewall, simon andrews (BI)
Re: [Gmod-schema] RE: Re: BioSQL or chado, Arnaud Kerhornou
Re: [Gmod-schema] RE: Re: BioSQL or chado, Chris Stoeckert
Re: [Gmod-schema] Re: Re: BioSQL or chado, David Emmert
RE: Re: BioSQL or chado, Nathan \(Nat\) Goodman
Re: Bioperl install tests behind firewall, Heikki Lehvaslaiho
Re: Bioperl install tests behind firewall, Jason Stajich
url of Pise has changed, Catherine Letondal
pdb.pm bug in atom/residue recognition, Dave Howorth
Bioperl install tests behind firewall, simon andrews (BI)
Re: Re: BioSQL or chado, Ewan Birney
Re: Re: BioSQL or chado, Hilmar Lapp
Re: [Gmod-schema] Re: BioSQL or chado, Allen Day
Re: BioSQL or chado, Steve Mathias
Re: BioSQL or chado, Chris Mungall
Re: filtering output from HTMLResultWriter, Jason Stajich
BioSQL or chado, Nathan \(Nat\) Goodman

July 29, 2003

filtering output from HTMLResultWriter, Charles Hauser
Re: MeSH terms in bioperl RE: (no subject), Hilmar Lapp
Re: Tree structure modification problems: Bug in remove_Descendent method, Babenko, Vladimir
Re: process_sgd.PLS trouble, Jason Stajich
process_sgd.PLS trouble, Venky Nandagopal
Re: MeSH terms in bioperl RE: (no subject), Heikki Lehvaslaiho
Re: RegSeq and NT_****** contig Id, Heikki Lehvaslaiho
Re: MeSH terms in bioperl RE: (no subject), Hilmar Lapp

July 28, 2003

List archives now searchable; feedback needed, Chris Dagdigian
Re: distant thoughts from a dinosaur..., Lincoln Stein
MeSH terms in bioperl RE: (no subject), Heikki Lehvaslaiho
Tree structure modification problems, Babenko, Vladimir

July 25, 2003

RE: distant thoughts from a dinosaur..., Chris Mungall
未承諾広告※まだ間に合う！, あきな
QRNA parser, Jason Stajich
Re: Position scoring matrix objects, Jason Stajich
Position scoring matrix objects, Stefan Kirov
Re: [Bioperl-guts-l] bioperl commit, Jason Stajich
Re: (no subject), Heikki Lehvaslaiho
(no subject), Christophe Bouvard
Re: Adding new sequence format to AlignIO module, Heikki Lehvaslaiho
Re: Problem using StandAloneFasta about 80000 times..., Palle Villesen (BiRC)

July 24, 2003

Adding new sequence format to AlignIO module, tulio de Oliveira
BioPerl behind WebMarshall firewall, Holland, Richard
Re: Bio::Graphics - roblem with heterogeneous_segments, Lincoln Stein
Re: [NT] Patch Submission (was: Problem using StandAloneFasta about 80000 times...), Ewan Birney
[NT] Patch Submission (was: Problem using StandAloneFasta about 80000 times...), Jonathan Barber
Re: Bioperl-1.2.2 installation fail on Mac Os 10.2.6, Jason Stajich
Bioperl-1.2.2 installation fail on Mac Os 10.2.6, Shin Enomoto
Re: Problem using StandAloneFasta about 80000 times..., Jason Stajich
new methods for Bio::Align::DNAStatistics, Richard Adams
Problem using StandAloneFasta about 80000 times..., Palle Villesen
RE: distant thoughts from a dinosaur..., Hilmar Lapp

July 23, 2003

Re: trans-spliced genes & gff2 & chado, Lincoln Stein
Re: SeqFeature containment hierarchies, Lincoln Stein
Re: RE: Bio Graphics - ppm install GD - error occurred, Lincoln Stein
Re: distant thoughts from a dinosaur..., Lincoln Stein
Re: Bio::Graphics::Glyph::translation magnification??, Lincoln Stein
SearchIO/blast.pm 1.2.2 bug, Jason Stajich
Bug in SearchIO in v 1.2.2, Gary Williams, Tel 01223 494522
Re: parsing an html blast result file, Jason Stajich
parsing an html blast result file, Wes Barris

July 22, 2003

Bio::Graphics - roblem with heterogeneous_segments, Dmitri Bichko
Re: testing for valid return from HTMLResultWriter, Jason Stajich
Updated my dpAlign module, Yee Man Chan
testing for valid return from HTMLResultWriter, Charles Hauser
Re: [Gmod-gbrowse] trans-spliced genes & gff2 & chado, Lincoln Stein
Re: Bio::PrimarySeq and Selenocysteine, Heikki Lehvaslaiho
Re: embl format, Ewan Birney
embl format, Michael R Olson
Re: installing bioperl on an SGI w/freeware perl, gcc, etc., Jason Stajich
Re: Bio::PrimarySeq and Selenocysteine, Lincoln Stein
Re: Bio::PrimarySeq and Selenocysteine, Heikki Lehvaslaiho
installing bioperl on an SGI w/freeware perl, gcc, etc., Wes Barris
Re: Module for McDonald-Kreitman, Jason Stajich

July 21, 2003

Module for McDonald-Kreitman, Jason Curole
Re: problems with libraries for Bio::Graphics, Lincoln Stein
parsing coded_by subfeature, Will Fischer
Bio::PrimarySeq and Selenocysteine, Lincoln Stein
Re: trans-spliced genes & gff2 & chado, Chris Mungall
Gap Penalties for BLOSUM62, William R.Pearson
Re: UCSC database -> GFF, Lincoln Stein
trans-spliced genes & gff2 & chado, Charles Hauser
problems with libraries for Bio::Graphics, Sergiy Ivakhno
Re: Converting Genbank to fasta via SeqIO, Heikki Lehvaslaiho
Converting Genbank to fasta via SeqIO, Wes Barris

July 20, 2003

Re: SeqFeature containment hierarchies, Hilmar Lapp
Re: parsing coded_by subfeature, Jack Chen
Re: parsing coded_by subfeature, Jason Stajich
Re: parsing coded_by subfeature, Jack Chen
Re: parsing coded_by subfeature, Jason Stajich
parsing coded_by subfeature, Jack Chen

July 19, 2003

RE: BioPerl CPAN, Nathan \(Nat\) Goodman

July 18, 2003

Re: UCSC database -> GFF, Paul Edlefsen
Re: What is the gap penalty function for BLOSUM62?, Yee Man Chan
RE: BioPerl CPAN, Allen Day
Re: UCSC database -> GFF, Ewan Birney
Re: What is the gap penalty function for BLOSUM62?, Ewan Birney

July 17, 2003

Re: What is the gap penalty function for BLOSUM62?, Aaron J Mackey
SeqFeature containment hierarchies, Chris Mungall
Re: UCSC database -> GFF, Paul Edlefsen
Re: UCSC database -> GFF, Allen Day
What is the gap penalty function for BLOSUM62?, Yee Man Chan
Re: module for unflattening GenBank/EMBL/DDBJ records, Chris Mungall
Re:All Non Profit Organizations, harvey65
RE: Bio Graphics - ppm install GD - error occurred, Nigam Shah
Re: quotes in features, Michael Muratet
Re: distant thoughts from a dinosaur..., Chris Mungall
RE: Re: Bio Graphics - ppm install GD - error occurred, Brian Osborne
RE: quotes in features, Brian Osborne
Re: Bio Graphics - ppm install GD - error occurred, Tanya Gray
Re: genbank chado loader or gff3 producer, Lincoln Stein
RE: BioPerl CPAN, Nathan \(Nat\) Goodman
RE: BioPerl CPAN, Ewan Birney
Re: quotes in features, Ewan Birney
quotes in features, Michael Muratet
Re: BioPerl CPAN, Ewan Birney
RE: bptutorial 24 bug, Brian Osborne
Re: module for unflattening GenBank/EMBL/DDBJ records, Peili Zhang
Re: BioPerl CPAN, Lincoln Stein
bptutorial 24 bug, albert vilella
interface to Darwin?, Matthew Betts
Re: genbank chado loader or gff3 producer, Scott Cain
Re: Version bug in GFF, bioperl 1.2.2, Andreas Kahari
Re: genbank chado loader or gff3 producer, Lincoln Stein
Re: Version bug in GFF, bioperl 1.2.2, Lincoln Stein
Re: UCSC database -> GFF, Lincoln Stein
Re: Indexing est fasta file., Lincoln Stein
Re: How do you change the default on Bio::DB::GenBank?, Lincoln Stein
Re: distant thoughts from a dinosaur..., Lincoln Stein
Re: Bio::Graphics::Glyph::translation magnification??, Lincoln Stein
Re: Bio::Graphics, Lincoln Stein
Re: Bio::DB::GFF, Lincoln Stein
Re: Bio Graphics, Lincoln Stein
Re: Bio::DB::Genbank Problem, Jason Stajich
Bio::DB::Genbank Problem, MArkus Kador

July 16, 2003

Bio::DB::GFF, Eley Greg
Re: Bio::DB::GFF trouble + Blast question, Venky Nandagopal
Re: BPN: BioPerl Nouveau [Was: Re: distant thoughts from a dinosaur...], Lincoln Stein
Re: Bio::DB::GFF trouble + Blast question, Lincoln Stein
Re: Hello LocusLink!!!, Heikki Lehvaslaiho
Re: Hello LocusLink!!!, Lincoln Stein
Hello LocusLink!!!, Line Neil
Re: Bio Graphics, Heikki Lehvaslaiho
Bio Graphics, Laurence Amilhat
Version bug in GFF, bioperl 1.2.2, Andreas Kahari
Re: Re: bacterial genome annotation, Marcus Claesson
Re: red hat 9 & perl bugs, Kris Boulez

July 15, 2003

new Bio::Restriction classes, Heikki Lehvaslaiho
Re: red hat 9 & perl bugs, Mike Muratet
Re: [Bioperl-guts-l] bioperl commit, Aaron J Mackey
Re: module for unflattening GenBank/EMBL/DDBJ records, Chris Mungall
red hat 9 & perl bugs, Charles Hauser
Re: Bio::Align::DNAStatistics extension?, Jason Stajich
Bio::Align::DNAStatistics extension?, Richard Adams
Re: bacterial genome annotation, Neil Saunders
Volunteer needed, no programming, Heikki Lehvaslaiho
Re: module for unflattening GenBank/EMBL/DDBJ records, Peili Zhang
Re: primer3 tests,files, Shawn Hoon
primer3 tests,files, Jason Stajich
Re: Re: RegSeq and NT_****** contig Id, Jason Stajich

July 14, 2003

Re: RegSeq and NT_****** contig Id, Heikki Lehvaslaiho

July 13, 2003

Re: help needed with __DATA__, Heikki Lehvaslaiho
Re: help needed with __DATA__, Shawn Hoon
help needed with __DATA__, Heikki Lehvaslaiho

July 12, 2003

Re: Help with testing of parallel Smith-Waterman code on x86 workstations, Nemo Physche

July 11, 2003

New restriction enzyme modules, Heikki Lehvaslaiho
Questions on module installation, Li, Qingqin [PRDUS]
Re: poblems with object's locations, Hilmar Lapp

July 10, 2003

RE: Indexing est fasta file., Ivan Sendin
how do I automatically update gene coordinates after re-sequencing, Marcus Claesson
RE: poblems with object's locations, Marc Logghe
poblems with object's locations, Sergiy Ivakhno
Re:For All Non Profit Organizations, limited_offer_actnow_nonprofit_only662191
mfold parser, Allen Day

July 09, 2003

Re: Using primer3, Shawn Hoon
HT search error, Stefan Kirov
Re: Using primer3, Mike Muratet
RE: Installation on Win32, Brian Osborne
RE: BioPerl CPAN & roadmap, Nathan \(Nat\) Goodman
Re: off by one problem w/exonerate & search2gff.pl ?, Jason Stajich
Installation on Win32, Pauline Ward
off by one problem w/exonerate & search2gff.pl ?, Charles Hauser
RE: Indexing est fasta file., Brian Osborne
Re: Using primer3, Shawn Hoon
Re: Using primer3, Heikki Lehvaslaiho
Re: Using primer3, Rob Edwards
PAML parsing, Jason Stajich
Re: Using primer3, Shawn Hoon

July 08, 2003

Re: specifying options in StandAloneBlast.pm, Jason Stajich
specifying options in StandAloneBlast.pm, Michael R Olson
Re: Help with testing of parallel Smith-Waterman code on x86 workstations, Jonathan Epstein
Re: Help with testing of parallel Smith-Waterman code on x86 workstations, Aaron J Mackey
Help with testing of parallel Smith-Waterman code on x86 workstations, Nemo Physche
Re: BPN: BioPerl Nouveau [Was: Re: distant thoughts from a dinosaur...], Hilmar Lapp
Re: Re: Bio::Tree::RandomFactory, Doug McLean
Using primer3, Mike Muratet
Re: distant thoughts from a dinosaur..., Steve Chervitz
Bioperl 1.2.2 released, Heikki Lehvaslaiho
Re: BPN: BioPerl Nouveau [Was: Re: distant thoughts from a dinosaur...], Heikki Lehvaslaiho
Re: BPN: BioPerl Nouveau [Was: Re: distant thoughts from a dinosaur...], Ewan Birney
Re: BPN: BioPerl Nouveau [Was: Re: distant thoughts from a dinosaur...], Aaron J Mackey
Re: BPN: BioPerl Nouveau [Was: Re: distant thoughts from a dinosaur...], Ewan Birney
Re: Makefile.PL, Heikki Lehvaslaiho
Re: BPN: BioPerl Nouveau [Was: Re: distant thoughts from a dinosaur...], Ewan Birney
Re: distant thoughts from a dinosaur..., Elia Stupka
Makefile.PL, Jason Stajich
Re: [Bioperl-guts-l] bioperl commit, Heikki Lehvaslaiho

July 07, 2003

BPN: BioPerl Nouveau [Was: Re: distant thoughts from a dinosaur...], Aaron J Mackey
Re: distant thoughts from a dinosaur..., Heikki Lehvaslaiho
Re: seq features with locations on remote entries?, Hilmar Lapp
Re: distant thoughts from a dinosaur..., Hilmar Lapp
distant thoughts from a dinosaur..., Ewan Birney
Re: How to represent no alignment?, Ewan Birney
Re: How to represent no alignment?, Jason Stajich
How to represent no alignment?, Yee Man Chan
[Bioperl-guts-l] Location of sequence text extractions (fwd), Jason Stajich
Re: seq features with locations on remote entries?, Matthew Betts

July 06, 2003

Re: bioperl-1.2.2 - Release Candidiate 2, Heikki Lehvaslaiho
Re: bioperl-1.2.2 - Release Candidiate 2, Rob Edwards
bioperl-1.2.2 - Release Candidiate 2, Heikki Lehvaslaiho

July 05, 2003

Re: How to Handle Parse Errors, Heikki Lehvaslaiho
Re: seq features with locations on remote entries?, Hilmar Lapp
Re: How to Handle Parse Errors, Hilmar Lapp
Bio::Index::Hmmer, Josh Lauricha

July 04, 2003

seq features with locations on remote entries?, Matthew Betts
cloning, upgrading, downgrading and conversion functionality, Marc Logghe
Re: How to Handle Parse Errors, Heikki Lehvaslaiho
How to Handle Parse Errors, dmcwilli
RE: Indexing est fasta file., Ivan Sendin
Re: Bio::DB::GFF trouble + Blast question, Scott Cain

July 03, 2003

Re: Bio::DB::GFF trouble + Blast question, Venky Nandagopal
Re: how to change the sequence of a Bio::Seq object, Hilmar Lapp
RE: how to change the sequence of a Bio::Seq object, Brian Osborne
Re: Bio::DB::GFF trouble + Blast question, Scott Cain
Re: how to change the sequence of a Bio::Seq object, Jason Stajich
RE: Indexing est fasta file., Brian Osborne
Re: Bio::DB::GFF trouble + Blast question, Venky Nandagopal
Indexing est fasta file., Ivan Sendin
Re: how to change the sequence of a Bio::Seq object, Peili Zhang
Re: how to change the sequence of a Bio::Seq object, Jason Stajich
how to change the sequence of a Bio::Seq object, Peili Zhang
Re: SeqFeature->_expand_region, Chris Mungall
Re: Bio::DB::GFF trouble + Blast question, Scott Cain
RE: BioPerl CPAN, Nathan \(Nat\) Goodman
Re: best coding practices, Hilmar Lapp
Re: best coding practices, Jason Stajich
Re: Bio::Tools::Run::Alignment::Clustalw in Bioperl 1.2?, Jason Stajich
Re: About handleing the UniGene database file, Jason Stajich
Re: Bio::DB::GenBank get_seq_by_acc, Heikki Lehvaslaiho
Re: Re: Bioperl-run release policy, Heikki Lehvaslaiho
Re: Bio::DB::GenBank get_seq_by_acc, Edith Schlagenhauf
Bio::DB::GenBank get_seq_by_acc, James Wasmuth
Re: Bioperl-run release policy, Shawn Hoon
Bio::DB::GFF trouble + Blast question, Venky Nandagopal
Re: SeqFeature->_expand_region, Heikki Lehvaslaiho
Bioperl-run release policy Re: Bio::Tools::Run::Alignment::Clustalw in Bioperl 1.2?, Heikki Lehvaslaiho
Re: SeqFeature->_expand_region, Hilmar Lapp
best coding practices, Hilmar Lapp
Re: Bio::Tools::Run::Alignment::Clustalw in Bioperl 1.2?, Shawn Hoon
Bio::Tools::Run::Alignment::Clustalw in Bioperl 1.2?, ��Х��
Bio::Tools::Run::Alignment::Clustalw in Bioperl 1.2?, ��Х��
About handleing the UniGene database file, darson
Re: SeqFeature->_expand_region, Hilmar Lapp
Re: SeqFeature->_expand_region, Chris Mungall
Re: SeqFeature->_expand_region, Hilmar Lapp
Re: How do you change the default on Bio::DB::GenBank?, Hilmar Lapp
Re: [personal] RE: How do you change the default on Bio::DB::GenBank?, Mark Wilkinson
RE: How do you change the default on Bio::DB::GenBank?, Jason Stajich
RE: How do you change the default on Bio::DB::GenBank?, Jason Stajich
Re: SeqFeature->_expand_region, Jason Stajich

July 02, 2003

RE: How do you change the default on Bio::DB::GenBank?, Mark Wilkinson
SeqFeature->_expand_region, Chris Mungall
RE: How do you change the default on Bio::DB::GenBank?, Hilmar Lapp
How do you change the default on Bio::DB::GenBank?, Mark Wilkinson
Re: get_Seq_by_acc() in Bio::DB::GeneBank failed, Gregory Wilson
Re: Sim4 output parsing using Bioperl, Jason Stajich
Re: Sim4 output parsing using Bioperl, Chris Mungall
Re: Bio::Ontology additions, Allen Day
Re: Sim4 output parsing using Bioperl, Hilmar Lapp
Re: Bio::Graphics, Josh Lauricha
Bio::Graphics, Josh Lauricha
Re: Bio::Ontology additions, Hilmar Lapp
Re: progress for 1.2.2 bugfix releae, Hilmar Lapp
Re: module for unflattening GenBank/EMBL/DDBJ records, Hilmar Lapp
Re: change the location coordinates of a Bio::SeqFeat ureI object, Hilmar Lapp
2003 CSHL Computational Genomics Course, William R. Pearson
Re: module for unflattening GenBank/EMBL/DDBJ records, Chris Mungall
Genbank interface changed, or is it just temporarily down?, Mark Wilkinson
Re: SignalP bug in predict_protein_features?, Shawn Hoon
SignalP bug in predict_protein_features?, david . vilanova
RE: searching pubmed, Brian Osborne
How to extract organism information from blast report?, Stefano Ghignone
problems with Biblio, Jonathan Yom-Tov
searching pubmed, Jonathan Yom-Tov

July 01, 2003

Re: Sim4 output parsing using Bioperl, Jason Stajich
Re: Sim4 output parsing using Bioperl, Jason Stajich
Re: Sim4 output parsing using Bioperl, Arnaud Kerhornou
How to extract organism information from blast report?, Stefano Ghignone
Re: Sim4 output parsing using Bioperl, Jason Stajich
Re: BioPerl CPAN, Jarkko Hietaniemi
Re: BioPerl CPAN, Steve Mathias
Re: Sim4 output parsing using Bioperl, Arnaud Kerhornou
Re: BioPerl CPAN, Jason Stajich
Re: BioPerl CPAN, Aaron J Mackey
VIRUS IN IHRER NACHRICHT AN bechtel@xxxxxxxx, virusmaster
Re: How to extract organism information from blast report?, ying lin
Re: BioPerl CPAN, Heikki Lehvaslaiho
Re: How to extract organism information from blast report?, Jason Stajich
Re: BioPerl CPAN, Jarkko Hietaniemi
Re: How to extract organism information from blast report?, ying lin
Re: BioPerl CPAN, Heikki Lehvaslaiho
Re: How to extract organism information from blast report?, Jason Stajich
How to extract organism information from blast report?, ying lin
Re: Nucleotide analysis modules - bugzilla # 1422, Heikki Lehvaslaiho
BioPerl CPAN, Nathan \(Nat\) Goodman
Re: bioperl-1.2.2 - Release Candidiate 1, Qiang TU
Re: bioperl-1.2.2 - Release Candidiate 1, Jason Stajich
bioperl-1.2.2 - Release Candidiate 1, Heikki Lehvaslaiho
Re: Sim4 output parsing using Bioperl, Jason Stajich
Re: Where could I find FISH Map information in mapview data or somewhere else?, Heikki Lehvaslaiho
Sim4 output parsing using Bioperl, Arnaud Kerhornou
Re: Where could I find FISH Map information in mapview data or somewhere else?, ole . st
Re: Where could I find FISH Map information in mapview data or somewhere else?, Heikki Lehvaslaiho
Where could I find FISH Map information in mapview data or somewhere else?, Sang Chul Choi

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