lang.perl.bio.general (thread)

progress for 1.2.2 bugfix releae, Jason Stajich
- Re: progress for 1.2.2 bugfix releae, Lincoln Stein
  - Re: progress for 1.2.2 bugfix releae, Heikki Lehvaslaiho
- Re: progress for 1.2.2 bugfix releae, Heikki Lehvaslaiho
- Re: progress for 1.2.2 bugfix releae, Aaron J Mackey
  - Re: progress for 1.2.2 bugfix releae, Aaron J Mackey
  - Re: progress for 1.2.2 bugfix releae, Heikki Lehvaslaiho
Can't get Bio::Tools::StandAloneBlast blastall to work in a cgi script, hackstam
- Re: Can't get Bio::Tools::StandAloneBlast blastall to work in a cgi script, Jason Stajich
Count amino acid frequency, Stephan Bour
- RE: Count amino acid frequency, Brian Osborne
  - Re: Count amino acid frequency, Stephan Bour
    - RE: Count amino acid frequency, Brian Osborne
    - Re: Count amino acid frequency, Stephan Bour
Bio::Graphics::Glyph::translation magnification??, Sofia
Bio::DB::Fasta, Michael R Olson
- RE: Bio::DB::Fasta, Brian Osborne
  - RE: Bio::DB::Fasta, Michael R Olson
    - RE: Bio::DB::Fasta, Brian Osborne
    - RE: Bio::DB::Fasta, Heikki Lehvaslaiho
Generating multiple fasta files from an embl file, Adam Witney
- RE: Generating multiple fasta files from an embl file, Brian Osborne
- Re: Generating multiple fasta files from an embl file, Jason Stajich
  - Re: Generating multiple fasta files from an embl file, Heikki Lehvaslaiho
    - RE: Generating multiple fasta files from an embl file, Brian Osborne
sequence upgrading, Marc Logghe
- Re: sequence upgrading, Hilmar Lapp
- RE: sequence upgrading, Marc Logghe
  - Re: sequence upgrading, Hilmar Lapp
- RE: sequence upgrading, Marc Logghe
  - RE: sequence upgrading, Heikki Lehvaslaiho
    - Re: sequence upgrading, Hilmar Lapp
  - Re: sequence upgrading, Hilmar Lapp
- RE: sequence upgrading, Marc Logghe
  - RE: sequence upgrading, Jamie Hatfield
- Re: sequence upgrading, Marc Logghe
- RE: sequence upgrading, Marc Logghe
RE: change the location coordinates of a Bio::SeqFeat ureI object, Marc Logghe
- RE: change the location coordinates of a Bio::SeqFeat ureI object, Jason Stajich
- RE: change the location coordinates of a Bio::SeqFeat ureI object, Peili Zhang
- RE: change the location coordinates of a Bio::SeqFeat ureI object, Peili Zhang
change the location coordinates of a Bio::SeqFeatureI object, Peili Zhang
StandAloneBlast (bl2seq) v. 2.2.6 problems, David Arenillas
Saving BLAST reports, Michael R Olson
- Re: Saving BLAST reports, Jason Stajich
ODBA Registry bugs , release 1.2.2 needed, Heikki Lehvaslaiho
- RE: ODBA Registry bugs , release 1.2.2 needed, Brian Osborne
- Re: ODBA Registry bugs , release 1.2.2 needed, Hilmar Lapp
  - Release plan for 1.2.2, Heikki Lehvaslaiho
    - Re: Release plan for 1.2.2, Catherine Letondal
    - Re: Release plan for 1.2.2, Jason Stajich
    - Re: Release plan for 1.2.2, Hilmar Lapp
sorting and indexing matricies, PD Schloss
- Re: sorting and indexing matricies, Morten Lindow
  - Re: sorting and indexing matricies, Shawn Hoon
- RE: sorting and indexing matricies, Marc Logghe
assembly assessment, Christie Robertson
Bio::Graphics help, June Tantoolvesm
- RE: Bio::Graphics help, Marc Logghe
Bio::SeqFeature::Gene::*, Josh Lauricha
- Re: Bio::SeqFeature::Gene::*, Jason Stajich
install 1.2.1 help newbie, Julian Dow
- RE: install 1.2.1 help newbie, Brian Osborne
using LargeSeq objects, Michael R Olson
- Re: using LargeSeq objects, Morten Lindow
  - RE: using LargeSeq objects, Brian Osborne
    - RE: using LargeSeq objects, Jason Stajich
    - RE: using LargeSeq objects, Brian Osborne
Nucleotide analysis modules - bugzilla # 1422, Rob Edwards
- Re: Nucleotide analysis modules - bugzilla # 1422, Hilmar Lapp
  - Re: Nucleotide analysis modules - bugzilla # 1422, Heikki Lehvaslaiho
- RE: Nucleotide analysis modules - bugzilla # 1422, Hilmar Lapp
  - Bio::Tools, Rob Edwards
    - Re: Bio::Tools, Jason Stajich
Bio::Ontology additions, Allen Day
- Re: Bio::Ontology additions, Hilmar Lapp
  - Re: Bio::Ontology additions, Allen Day
Re: Bio::Tree::RandomFactory, Ewan Birney
- Re: Re: Bio::Tree::RandomFactory, Jason Stajich
srsperl.pm, Sunitha Thodupunuri
- Re: srsperl.pm, Heikki Lehvaslaiho
Please unscribe me, email hesn@xxxxxxxxxxxx, Suiwen He
Bioperl Dependancies, Sunitha Thodupunuri
- Re: Bioperl Dependancies, Lincoln Stein
- RE: Bioperl Dependancies, Marc Logghe
module for unflattening GenBank/EMBL/DDBJ records, Chris Mungall
- Re: module for unflattening GenBank/EMBL/DDBJ records, Ewan Birney
  - Re: module for unflattening GenBank/EMBL/DDBJ records, Chris Mungall
    - Re: module for unflattening GenBank/EMBL/DDBJ records, Jason Stajich
    - Re: module for unflattening GenBank/EMBL/DDBJ records, Lincoln Stein
    - Re: module for unflattening GenBank/EMBL/DDBJ records, Ewan Birney
    - Re: module for unflattening GenBank/EMBL/DDBJ records, Chris Mungall
    - Re: module for unflattening GenBank/EMBL/DDBJ records, Hilmar Lapp
- Re: module for unflattening GenBank/EMBL/DDBJ records, Lincoln Stein
RE: Bio::FeatureHolderI interface confusion (Hilmar Lapp), Nathan \(Nat\) Goodman
- Re: RE: Bio::FeatureHolderI interface confusion (Hilmar Lapp), Hilmar Lapp
  - RE: RE: Bio::FeatureHolderI interface confusion (Hilmar Lapp), Nathan \(Nat\) Goodman
    - Re: RE: Bio::FeatureHolderI interface confusion, Hilmar Lapp
    - BioPAN, Heikki Lehvaslaiho
    - RE: BioPAN, Nathan \(Nat\) Goodman
    - Re: RE: BioPAN, Heikki Lehvaslaiho
BioSQL: loading large sequence records, and taxon parsing, Xiaoying Lin
- Re: BioSQL: loading large sequence records, and taxon parsing, Hilmar Lapp
  - plastid genetic code (was: BioSQL: loading large sequence records, and taxon parsing), Will Fischer
- BioSQL: loading large sequence records, and taxon parsing, Xiaoying Lin
  - Re: BioSQL: loading large sequence records, and taxon parsing, Hilmar Lapp
  - Re: BioSQL: loading large sequence records, and taxon parsing, Juguang Xiao
    - Re: BioSQL: loading large sequence records, and taxon parsing, Elia Stupka
    - Re: BioSQL: loading large sequence records, and taxon parsing, Hilmar Lapp
- RE: BioSQL: loading large sequence records, and taxon parsing, Lin, Xiaoying
- RE: BioSQL: loading large sequence records, and taxon parsing, Hilmar Lapp
- RE: BioSQL: loading large sequence records, and taxon parsing, Hilmar Lapp
proposed change to Bio::SeqFeature::Gene::*, Chris Mungall
- RE: proposed change to Bio::SeqFeature::Gene::*, Hilmar Lapp
  - Re: [BioPerl] RE: proposed change to Bio::SeqFeature::Gene::*, Mark Wilkinson
    - Re: [BioPerl] RE: proposed change to Bio::SeqFeature::Gene::*, Chris Mungall
  - Re: proposed change to Bio::SeqFeature::Gene::*, Lincoln Stein
    - Re: [BioPerl] Re: proposed change to Bio::SeqFeature::Gene::*, Mark Wilkinson
    - Re: proposed change to Bio::SeqFeature::Gene::*, Chris Mungall
    - Re: proposed change to Bio::SeqFeature::Gene::*, Lincoln Stein
    - Re: proposed change to Bio::SeqFeature::Gene::*, Paul Edlefsen
    - Re: proposed change to Bio::SeqFeature::Gene::*, Ewan Birney
    - Re: proposed change to Bio::SeqFeature::Gene::*, Ewan Birney
  - Re: proposed change to Bio::SeqFeature::Gene::*, David Block
    - Re: [Hackathon] Re: proposed change to Bio::SeqFeature::Gene::*, Mark Wilkinson
    - Re: [Hackathon] Re: proposed change to Bio::SeqFeature::Gene::*, Lincoln Stein
    - Re: [Hackathon] Re: proposed change to Bio::SeqFeature::Gene::*, Mark Wilkinson
    - Re: [Hackathon] Re: proposed change to Bio::SeqFeature::Gene::*, Chris Mungall
Bio::FeatureHolderI interface confusion, Chris Mungall
- Re: Bio::FeatureHolderI interface confusion, Ewan Birney
  - Re: Bio::FeatureHolderI interface confusion, Chris Mungall
    - Re: Bio::FeatureHolderI interface confusion, Lincoln Stein
- RE: Bio::FeatureHolderI interface confusion, Hilmar Lapp
  - RE: Bio::FeatureHolderI interface confusion, Chris Mungall
    - Re: Bio::FeatureHolderI interface confusion, Lincoln Stein
    - Re: Bio::FeatureHolderI interface confusion, Chris Mungall
    - Re: Bio::FeatureHolderI interface confusion, Lincoln Stein
    - Re: Bio::FeatureHolderI interface confusion, Chris Mungall
    - Re: Bio::FeatureHolderI interface confusion, Hilmar Lapp
    - Re: Bio::FeatureHolderI interface confusion, Paul Edlefsen
    - Re: Bio::FeatureHolderI interface confusion, Hilmar Lapp
    - Re: Bio::FeatureHolderI interface confusion, Hilmar Lapp
    - Re: Bio::FeatureHolderI interface confusion, Chris Mungall
    - Re: [Hackathon] Re: Bio::FeatureHolderI interface confusion, Mark Wilkinson
    - Re: Bio::FeatureHolderI interface confusion, Ewan Birney
    - Re: Bio::FeatureHolderI interface confusion, Hilmar Lapp
    - Re: Bio::FeatureHolderI interface confusion, Paul Edlefsen
    - Re: Bio::FeatureHolderI interface confusion, Hilmar Lapp
    - Re: Bio::FeatureHolderI interface confusion, Matthew Pocock
  - Message not available
    - RE: Bio::FeatureHolderI interface confusion, Peter Wilkinson
    - Re: Bio::FeatureHolderI interface confusion, Hilmar Lapp
  - RE: Bio::FeatureHolderI interface confusion, Steve Mathias
- RE: Bio::FeatureHolderI interface confusion, Nathan \(Nat\) Goodman
  - Re: RE: Bio::FeatureHolderI interface confusion, Ewan Birney
    - RE: RE: Bio::FeatureHolderI interface confusion, Nathan \(Nat\) Goodman
    - RE: RE: Bio::FeatureHolderI interface confusion, Ewan Birney
    - Re: RE: Bio::FeatureHolderI interface confusion, Steve Chervitz
    - RE: Bio::FeatureHolderI interface confusion, Nathan \(Nat\) Goodman
    - Re: Bio::FeatureHolderI interface confusion, Steve Chervitz
    - RE: BioPAN, Steve Mathias
  - RE: Bio::FeatureHolderI interface confusion, Chris Mungall
    - Re: Bio::FeatureHolderI interface confusion, Paul Edlefsen
    - Re: Re: Bio::FeatureHolderI interface confusion, Lincoln Stein
UCSC database -> GFF, Paul Edlefsen
- Re: UCSC database -> GFF, Jason Stajich
  - Re: UCSC database -> GFF, Paul Edlefsen
  - Re: UCSC database -> GFF, Lincoln Stein
    - Re: UCSC database -> GFF, Allen Day
    - Re: UCSC database -> GFF, Lincoln Stein
    - Re: UCSC database -> GFF, Ewan Birney
    - Re: UCSC database -> GFF, Hilmar Lapp
    - Re: UCSC database -> GFF, Paul Edlefsen
    - Re: UCSC database -> GFF, Allen Day
    - Re: UCSC database -> GFF, Paul Edlefsen
- Re: UCSC database -> GFF, Allen Day
Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Jason Stajich
- Re: Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Lincoln Stein
  - Re: Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Ewan Birney
- Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Chris Mungall
- Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Peili Zhang
  - Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Jason Stajich
- Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Peili Zhang
  - Re: Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Jason Stajich
  - Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Chris Mungall
    - Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Jason Stajich
    - Re: Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Lincoln Stein
- Re: Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Peili Zhang
  - Re: Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Chris Mungall
- Re: [Bioperl-announce-l] an extension to Bio::SeqIO, Peili Zhang
- Re: [Bioperl-announce-l] an extension to Bio::SeqIO, SLetovsky
Problem installing staden io_lib, Andreas Boehm
- Re: Problem installing staden io_lib, Aaron J Mackey
How to use Proxy in Bioperl programming?, du
Re: stale links, EMBL loading, Hilmar Lapp
- Re: Re: stale links, EMBL loading, Niels Larsen
  - Re: Re: stale links, EMBL loading, Hilmar Lapp
GFF3 Specification, Lincoln Stein
New to Bioperl, Niels Larsen
- Re: New to Bioperl, Hilmar Lapp
Report to Recipient(s), QOLOTUS00
call bioperl methods from java, Sally Li
- Re: call bioperl methods from java, Aaron J Mackey
Re: get_Seq_by_acc() in Bio::DB::GeneBank failed, jun hu
Bio::Tools::Genscan initialization ?, Bryony Lloyd
- Re: Bio::Tools::Genscan initialization ?, Jason Stajich
get_Seq_by_acc() in Bio::DB::GeneBank failed, jun hu
- Re: get_Seq_by_acc() in Bio::DB::GeneBank failed, Qunfeng Dong
How to retrieve introns / exons from EMBL?, Ole Schulz-Trieglaff
- RE: How to retrieve introns / exons from EMBL?, Brian Osborne
  - RE: How to retrieve introns / exons from EMBL?, ole . st
    - RE: How to retrieve introns / exons from EMBL?, Jason Stajich
    - RE: How to retrieve introns / exons from EMBL?, Ole Schulz-Trieglaff
    - RE: How to retrieve introns / exons from EMBL?, Jason Stajich
    - RE: How to retrieve introns / exons from EMBL?, Ole Schulz-Trieglaff
from protein to nucleotide, Jack Chen
- RE: from protein to nucleotide, Marc Logghe
  - RE: from protein to nucleotide, Jason Stajich
How to get refseq sequence object?, Jack Chen
- Re: How to get refseq sequence object?, Jason Stajich
GenPept, jkrzywin
Re: cpu time contribution, Catherine Letondal
how to get the database name for Bio::Seq->accession_number?, Peili Zhang
retreive GenBank Seq - the same script always worked before but now ..., Qunfeng Dong
- Re: retreive GenBank Seq - the same script always worked before but now ..., Heikki Lehvaslaiho
Statistical Methods in Bioinformatics: An Introduction, Serge Ivahno
Re:Smith waterman Alignment, M K. Govind
- Re: Re:Smith waterman Alignment, Ewan Birney
Bio::DB::GFF and Gadfly GFFs question, Venky Nandagopal
- Re: Bio::DB::GFF and Gadfly GFFs question, Jason Stajich
Sequence Validation, Matthew Laird
- Re: Sequence Validation, Jason Stajich
  - Re: Sequence Validation, Matthew Laird
    - RE: Sequence Validation, Brian Osborne
    - validate_seq() note, Brian Osborne
    - RE: Sequence Validation, Matthew Laird
    - RE: Sequence Validation, Jason Stajich
    - Re: Sequence Validation, Hilmar Lapp
- RE: Sequence Validation, Hilmar Lapp
  - RE: Sequence Validation, Jason Stajich
- sequence validation, William R.Pearson
  - Re: sequence validation, Joel Martin
wwwblast standalone, Line Neil
- Re: wwwblast standalone, Sang Chul Choi
Eclipse Perl IDE (EPIC), Steve Chervitz
blastall and blosum62 problem, Mariano Latorre A
- Re: blastall and blosum62 problem, Jason Stajich
- Re: blastall and blosum62 problem, Ian Korf
Bio::DB:: queries, Jason Stajich
- Re: Bio::DB:: queries, Prachi Shah
  - Re: Bio::DB:: queries, Jason Stajich
- Re: Bio::DB:: queries, Qing Lyne Gao
- RE: Bio::DB:: queries, Hilmar Lapp
- Re: Bio::DB:: queries, Jonathan Epstein
(no subject), Jason Stajich
- perl <-> java [was Re: (no subject)], Juguang Xiao
  - Re: perl <-> java [was Re: (no subject)], Stephen Montgomery
    - Re: perl <-> java [was Re: (no subject)], Juguang Xiao
  - Is this a bug?, Sally Li
Re: OBDA/Flat question, Elia Stupka
- RE: OBDA/Flat question, Brian Osborne
  - RE: OBDA/Flat question, Heikki Lehvaslaiho
    - RE: OBDA/Flat question, Brian Osborne
  - Re: OBDA/Flat question, Lincoln Stein
- RE: OBDA/Flat question, Hilmar Lapp
Running remote blast example, Vikas Daga
- Re: Running remote blast example, Vikas Daga
  - Re: Running remote blast example, Vikas Daga
strand() question, hackstam
- RE: strand() question, Brian Osborne
  - Re: strand() question, Steve Chervitz
    - Re: strand() question, Jason Stajich
    - Re: strand() question, Steve Chervitz
RE: NCBI fasta format [was: Re: loading data intobioperl-db], Cook, Malcolm
- RE: NCBI fasta format [was: Re: loading data intobioperl-db], Peter Wilkinson
  - Re: NCBI fasta format [was: Re: loading data intobioperl-db], Matthew Pocock
Re: [Bioperl-guts-l] bioperl commit, Sally Li
acc does not exist, Brent and Johnetta Smith
- Re: acc does not exist, Heikki Lehvaslaiho
- RE: acc does not exist, Brian Osborne
how to use BioQuery, Michael Thon
- Re: how to use BioQuery, Hilmar Lapp
  - Re: how to use BioQuery, Juguang Xiao
    - Re: how to use BioQuery, Hilmar Lapp
RE: NCBI fasta format [was: Re: loading data into bioperl-db], Hilmar Lapp
- RE: NCBI fasta format [was: Re: loading data into bioperl-db], Aaron J Mackey
  - Re: NCBI fasta format [was: Re: loading data into bioperl-db], Hilmar Lapp
  - Re: NCBI fasta format [was: Re: loading data into bioperl-db], Hilmar Lapp
    - Re: NCBI fasta format [was: Re: loading data into bioperl-db], Aaron J Mackey
rank in bioperl-db PersistentObjectI, Michael Thon
- RE: rank in bioperl-db PersistentObjectI, Hilmar Lapp
Fixed the previously reported BLAST query length issue, Matthew Vaughn
- Re: Fixed the previously reported BLAST query length issue, Jason Stajich
Parsing BLASTP or TBLASTN reveals subtle query_length = 0 bug, Matthew Vaughn
bl2seq parse nightmare, Julio Fernandez Banet
- Re: bl2seq parse nightmare, Jason Stajich
Problem with load_seqdatabase, albert vilella
SearchIO::blast.pm developer notes, Steve Chervitz
cvs hanging ..., Aaron J Mackey
- Re: cvs hanging ..., Steve Chervitz
Re: passing multiple databases to blastall, Andrew Nunberg
- Re: passing multiple databases to blastall, Paul Boutros
Query seq with gaps in blast, Julio Fernandez Banet
loading data into bioperl-db, Michael Thon
- Re: loading data into bioperl-db, Hilmar Lapp
  - Re: loading data into bioperl-db, Michael Thon
    - Re: loading data into bioperl-db, Hilmar Lapp
    - NCBI fasta format [was: Re: loading data into bioperl-db], Aaron J Mackey
    - Re: NCBI fasta format [was: Re: loading data into bioperl-db], Peter Wilkinson
    - Re: NCBI fasta format [was: Re: loading data into bioperl-db], Aaron J Mackey
Merged my code with bioprrl-ext-06, Yee Man Chan
- Re: Merged my code with bioprrl-ext-06, Aaron J Mackey
  - Re: Merged my code with bioprrl-ext-06, Yee Man Chan
    - Re: Merged my code with bioprrl-ext-06, Aaron J Mackey
  - Re: Merged my code with bioprrl-ext-06, Yee Man Chan
problem with batch access to GenBank, Anne-Marie Ternes
- RE: problem with batch access to GenBank, Brian Osborne
  - Re: problem with batch access to GenBank, Anne-Marie Ternes
bl2seq error when no alignment, Julio Fernandez Banet
- Re: bl2seq error when no alignment, Jason Stajich
bad link in bioperl.org, Juguang Xiao
- RE: bad link in bioperl.org, Brian Osborne
Multiple genbank-formatted entries in a single file, Babenko, Vladimir
newick parsing internally labeled nodes, Jason Stajich
Global version number for all bioperl modules, Heikki Lehvaslaiho
- Re: Global version number for all bioperl modules, Hilmar Lapp
- Re: Global version number for all bioperl modules, Heikki Lehvaslaiho
  - Re: Global version number for all bioperl modules, Aaron J Mackey
    - Re: Global version number for all bioperl modules, Heikki Lehvaslaiho
- Re: Global version number for all bioperl modules, Donald G. Jackson
  - Re: Global version number for all bioperl modules, Heikki Lehvaslaiho
Whitespace in locus causes problems for parsers, Michael Muratet
- Fw: RE: Whitespace in locus causes problems for parsers, Michael Muratet
Re: problems by installing bioperl, Heikki Lehvaslaiho
Re: How can I edit a sequence?, Heikki Lehvaslaiho
- Re: How can I edit a sequence?, Heikki Lehvaslaiho
  - Re: How can I edit a sequence?, Yee Man Chan
Re: One more odd little parsing problem for your list, Hilmar Lapp
- Re: One more odd little parsing problem for your list, Heikki Lehvaslaiho
Re: bioperl-run 1.2.0 tarball available, Catherine Letondal
Added install methods to makefile, Lincoln Stein
- Re: Added install methods to makefile, Hilmar Lapp
  - Re: Added install methods to makefile, Heikki Lehvaslaiho
Re: Changing extent of Bio::Graphics::Panel, Lincoln Stein