lang.perl.bio.general (thread)

Searching the mailing list archives, Kerr Wall
- RE: Searching the mailing list archives, Brian Osborne
Bioperl 1.2 Released, Ewan Birney
Error from Blast, Andy Nunberg
GenBank Parser, Drew Stewart
- Re: GenBank Parser, Ewan Birney
- Re: GenBank Parser, Hilmar Lapp
bug squashing, Hilmar Lapp
- Re: bug squashing, Ewan Birney
Documentation tweaks; Release Candidate 1 up, Ewan Birney
- Re: Documentation tweaks; Release Candidate 1 up, Peter Schattner
  - Re: Documentation tweaks; Release Candidate 1 up, Ewan Birney
    - Re: Documentation tweaks; Release Candidate 1 up, Peter Schattner
- Re: Documentation tweaks; Release Candidate 1 up, Paul Boutros
  - Re: Documentation tweaks; Release Candidate 1 up, Hilmar Lapp
    - Re: Documentation tweaks; Release Candidate 1 up, Elia Stupka
More fixes; next 5 days, Ewan Birney
Query for parseing Genbank files with BioGraphics, Soumyadeep nandi
Specifying restriction enzyme with cut site outside recognition sequence, Alexander Gimelbrant
- Re: Specifying restriction enzyme with cut site outside recognition sequence, Steve Chervitz
mapping UniGene IDs to GO ids, Jonathan Epstein
- Re: mapping UniGene IDs to GO ids, Paul Boutros
Handleing OS differences, Scott Cain
- Re: Handleing OS differences, Hilmar Lapp
Re remote blast, Clement Mesdon
- Re: Re remote blast, Ewan Birney
  - Re bioinf books, David Messina
- RE: Re remote blast, nkuipers
Remote Blast, Clement Mesdon
- RE: Remote Blast, nkuipers
RE: Bioperl 1.2.alpha testing under cygwin. Was RE: [Bioperl-l] 1.2- alpha-1 tar file built, Nash, John
- RE: Bioperl 1.2.alpha testing under cygwin. Was RE: [Bioperl-l] 1.2- alpha-1 tar file built, Nash, John
  - Re: RE: Bioperl 1.2.alpha testing under cygwin. Was RE: [Bioperl-l] 1.2- alpha-1 tar file built, Ewan Birney
Happy Christmasl; More testing please!, Ewan Birney
- Re: Happy Christmasl; More testing please!, Jason Stajich
  - Re: Happy Christmasl; More testing please!, Ewan Birney
Genbank/EMBL output, Alex Hudek
- Re: Genbank/EMBL output, Hilmar Lapp
  - Re: Genbank/EMBL output, Alex Hudek
Bioperl 1.2.alpha testing under cygwin. Was RE: 1.2- alpha-1 tar file built, Nash, John
- Re: Bioperl 1.2.alpha testing under cygwin. Was RE: [Bioperl-l] 1.2- alpha-1 tar file built, Ewan Birney
Bio::Assembly::IO::ace with CAP3 ace files, Marc Logghe
- Re: Bio::Assembly::IO::ace with CAP3 ace files, Ewan Birney
  - Re: Bio::Assembly::IO::ace with CAP3 ace files, Robson Francisco de Souza
Question - Primary_id, Ewan Birney
- Re: Question - Primary_id, Hilmar Lapp
  - Re: Question - Primary_id, Ewan Birney
    - Re: Question - Primary_id, Hilmar Lapp
Parsing for Bioinformatics class with Damian Conway, Uri Guttman
- Re: Parsing for Bioinformatics class with Damian Conway, Ewan Birney
Make test please...., Ewan Birney
- Bio::Graphics off-by-one error at high magnification, Lincoln Stein
thanks to all and sundry, nkuipers
SearchIO on Blast error, Brian Carlson
- Re: SearchIO on Blast error, Jason Stajich
- RE: SearchIO on Blast error, Brian Carlson
windows+ppm user dev needed, Jason Stajich
Correct SearchIO usage, Brian Carlson
- Re: Correct SearchIO usage, Jason Stajich
Question about Bio::SearchIO behavior, Donald G. Jackson
- Re: Question about Bio::SearchIO behavior, Jason Stajich
Bioperl Makefile.PL and testing, Chad Matsalla
- Re: Bioperl Makefile.PL and testing, Ewan Birney
- Re: Bioperl Makefile.PL and testing, Hilmar Lapp
sequence trace index data, Chad Matsalla
- Re: sequence trace index data, Ewan Birney
  - Re: sequence trace index data, Robson Francisco de Souza
    - Re: sequence trace data, Chad Matsalla
    - Re: sequence trace data, Robson Francisco de Souza
Newbie...., Brian Carlson
Bptutorial.pl, Paul Boutros
- Re: Bptutorial.pl, Peter Schattner
  - Re: Bptutorial.pl, Paul Boutros
    - Re: Bptutorial.pl, Peter Schattner
    - Re: Bptutorial.pl, Jason Stajich
    - Re: Bptutorial.pl, Peter Schattner
    - Re: Bptutorial.pl, Jason Stajich
    - Re: Bptutorial.pl, Jason Stajich
    - Re: Bptutorial.pl, Peter Schattner
Bundle::BioPerl under cygwin Was: Ace failure, Nash, John
What is a Bioinformatics API?, Chester Langin
[Bioinformatics] iPod and A/G BLAST (fwd), Eugen Leitl
- Re: [Bioinformatics] iPod and A/G BLAST (fwd), Aaron J Mackey
- Re: [Bioinformatics] iPod and A/G BLAST (fwd), Hilmar Lapp
installing Bio::DB::GFF, Chester Langin
- Re: installing Bio::DB::GFF, Jason Stajich
Removing duplicate FASTA record one-liners, William R.Pearson
- Re: Removing duplicate FASTA record one-liners, Paul Gordon
  - Re: Removing duplicate FASTA record one-liners, Lincoln Stein
Ace failure, Chester Langin
- Re: Ace failure, Lincoln Stein
  - Re: Ace failure, Ewan Birney
    - Re: Ace failure, Chris Dagdigian
    - Re: Ace failure, Jonathan Epstein
    - Re: Ace failure, Lincoln Stein
XML::Writer test seg fault, Chester Langin
- Re: XML::Writer test seg fault, Jason Stajich
- Re: XML::Writer test seg fault, Robin Berjon
removing duplicate fasta records, Amit Indap <indapa@xxxxxxxxxxxxxx>
- Re: removing duplicate fasta records, Lincoln Stein
- RE: removing duplicate fasta records, nkuipers
- RE: removing duplicate fasta records, Marc Logghe
- Re: removing duplicate fasta records, Jonathan Epstein
  - Re: removing duplicate fasta records, Paul Gordon
    - Re: removing duplicate fasta records, Ewan Birney
    - Re: removing duplicate fasta records, Michal Kurowski
    - Re: Re: removing duplicate fasta records, Lincoln Stein
    - Re: Re: removing duplicate fasta records, Ewan Birney
    - Re: removing duplicate fasta records, James Wasmuth
    - Re: Now very OT: removing duplicate fasta records, Sam Griffiths-Jones
    - Re: Now very OT: removing duplicate fasta records, Ewan Birney
- Re: removing duplicate fasta records, Paul Boutros
- Re: removing duplicate fasta records, Simon K. Chan
1.2-alpha-1 tar file built, Ewan Birney
- Re: 1.2-alpha-1 tar file built, Chris Dagdigian
- RE: 1.2-alpha-1 tar file built, Nash, John
  - RE: 1.2-alpha-1 tar file built, Ewan Birney
Bio::SearchIO $hit->description(), only one line returned..., Martin Schenker
- Re: Bio::SearchIO $hit->description(), only one line returned..., Jason Stajich
  - Re: Bio::SearchIO $hit->description(), only one line returned..., Ewan Birney
[Bioinformatics] First Genetic Trust to build Open-Source Gene-Expression tools (fwd), Eugen Leitl
Query for parsing BLAST with BioGraphics, Soumyadeep nandi
- Re: Query for parsing BLAST with BioGraphics, Lincoln Stein
Representation of phylogenetic trees, Jutta Buschbom
- RE: Representation of phylogenetic trees, Marc Logghe
  - RE: Representation of phylogenetic trees, Jason Stajich
    - Re: Representation of phylogenetic trees, David Messina
    - Re: Representation of phylogenetic trees, Hilmar Lapp
    - Re: Representation of phylogenetic trees, Hilmar Lapp
    - Re: Representation of phylogenetic trees, David Messina
- Re: Representation of phylogenetic trees, Jutta Buschbom
[Bioperl-guts-l] [Bug 1355] Segmentation error from Bio::Index::Fasta (fwd), Jason Stajich
List summary: Dec 9-15, 2002, Nathan Torkington
- RE: List summary: Dec 9-15, 2002, Hilmar Lapp
  - RE: List summary: Dec 9-15, 2002, Elia Stupka
    - RE: List summary: Dec 9-15, 2002, Xiao Juguang
    - RE: List summary: Dec 9-15, 2002, Jason Stajich
    - Re: desc/description, Hilmar Lapp
    - Re: List summary: Dec 9-15, 2002, Hilmar Lapp
changes in standaloneblast, Phillip Lord
- Re: changes in standaloneblast, Jason Stajich
  - Re: changes in standaloneblast, Phillip Lord
  - help extracting CDS, Pedro Antonio Reche
    - Re: help extracting CDS, Jason Stajich
    - Re: help extracting CDS, Pedro Antonio Reche
    - Re: Re: help extracting CDS, Jason Stajich
    - Re: Re: help extracting CDS, Rob Edwards
    - Re: Re: help extracting CDS, Hilmar Lapp
    - Re: Re: help extracting CDS, Hilmar Lapp
  - Message not available
    - Unsubscribe?, Joao Magalhaes
    - Re: Unsubscribe?, David Messina
Root DESTROY flip; All tests pass, Ewan Birney
- Re: Root DESTROY flip; All tests pass, Lincoln Stein
  - Query re segementation error from Bio::Index::Fasta, Peter Schattner
    - Re: Query re segementation error from Bio::Index::Fasta, Jason Stajich
    - Re: Query re segementation error from Bio::Index::Fasta, Lincoln Stein
    - Re: Query re segementation error from Bio::Index::Fasta, Peter Schattner
RE: Parsing sequence records in memory, Marc Logghe
All tests pass, Ewan Birney
- Re: All tests pass, Paul Boutros
  - Re: All tests pass, Jason Stajich
  - Re: All tests pass, Jason Stajich
    - Re: All tests pass, Paul Boutros
    - Re: All tests pass, Ewan Birney
Makefile; Funkiness with _rearrange issues and - on alignments, Ewan Birney
- Re: Makefile; Funkiness with _rearrange issues and - on alignments, Lincoln Stein
- Re: Makefile; Funkiness with _rearrange issues and - on alignments, Hilmar Lapp
  - Re: Makefile; Funkiness with _rearrange issues and - on alignments, Aaron J Mackey
    - Re: Makefile; Funkiness with _rearrange issues and - on alignments, Ewan Birney
    - Re: Makefile; Funkiness with _rearrange issues and - on alignments, Aaron J Mackey
This may help someone install bioperl, Pierre Far
RE: Should be simple accession number script, but it' s not., Marc Logghe
- Re: Should be simple accession number script, but it' s not., Lincoln Stein
Should be simple accession number script, but it's not., Agrin, Nathan
- Re: Should be simple accession number script, but it's not., Ewan Birney
- RE: Should be simple accession number script, but it's not., Jamie Hatfield
  - RE: Should be simple accession number script, but it's not., Jason Stajich
    - RE: Should be simple accession number script, but it's not., Jamie Hatfield
    - Re: Should be simple accession number script, but it's not., Lincoln Stein
Bio::Tools::Run::StandAloneBlast temporary file, Marc Logghe
How good is Bio::Assembly::IO::ace ?, Lu, Hong
- Re: How good is Bio::Assembly::IO::ace ?, Jason Stajich
- Re: How good is Bio::Assembly::IO::ace ?, Robson Francisco de Souza
- Re: How good is Bio::Assembly::IO::ace ?, Ewan Birney
Sending Accession Numbers to Blast Server, Agrin, Nathan
- Re: Sending Accession Numbers to Blast Server, Jason Stajich
Potential Bug assignments:, Ewan Birney
- Re: Potential Bug assignments:, Lincoln Stein
  - Re: Potential Bug assignments:, Ewan Birney
    - Re: Potential Bug assignments:, Lincoln Stein
- Re: Potential Bug assignments:, Peter Schattner
- Parsing sequence records in memory, Peter Schattner
  - Re: Parsing sequence records in memory, Ewan Birney
    - Re: Parsing sequence records in memory, Jason Stajich
Old documentation, Michael Muratet
BioGraphics, soumyadeep nandi
- a littlet bit inconsistency in Bio::SeqFeature::Generic, Xiao Juguang
  - Re: a littlet bit inconsistency in Bio::SeqFeature::Generic, Hilmar Lapp
    - Re: a littlet bit inconsistency in Bio::SeqFeature::Generic, Xiao Juguang
    - Re: a littlet bit inconsistency in Bio::SeqFeature::Generic, Mark Wilkinson
- Re: BioGraphics, Lincoln Stein
documentation changes, Allen Day
- Re: documentation changes, Peter Schattner
  - Re: documentation changes, Ewan Birney
List Summary for Dec 2-8 2002, Nathan Torkington
List summaries, Nathan Torkington
- Re: List summaries, Kutbuddin Doctor
  - Re: Re: List summaries, Nathan Torkington
  - Re: Re: List summaries, Ewan Birney
sample code for Bio::Phenotype::OMIM::OMIMparser, Leonardo Kenji Shikida
- Re: sample code for Bio::Phenotype::OMIM::OMIMparser, Leonardo Kenji Shikida
- RE: sample code for Bio::Phenotype::OMIM::OMIMparser, Hilmar Lapp
- RE: sample code for Bio::Phenotype::OMIM::OMIMparser, Chris Zmasek
[Bioperl-guts-l] Notification: incoming/1325 (fwd), Jason Stajich
end < start?, Estienne Swart
which version is installed, Jason Stajich
- Re: which version is installed, Allen Day
- RE: which version is installed, Hilmar Lapp
  - RE: which version is installed, Allen Day
    - Re: which version is installed, Hilmar Lapp
    - Re: which version is installed (and links to documentation projects), Allen Day
    - Re: which version is installed (and links to documentation projects), Jason Stajich
    - Re: which version is installed (and links to documentation projects), Allen Day
    - Re: which version is installed, Ewan Birney
Re: LocusLink IO, Paul Boutros
- RE: LocusLink IO, Hilmar Lapp
  - RE: LocusLink IO, Paul Boutros
- RE: LocusLink IO, Hilmar Lapp
Bio::Index question, Stephen Wang
- RE: Bio::Index question, Hilmar Lapp
BLASTing BioSeq objects, James Wasmuth
- Re: BLASTing BioSeq objects, Shawn
  - Re: BLASTing BioSeq objects, James Wasmuth
    - Re: BLASTing BioSeq objects, Shawn
    - Re: BLASTing BioSeq objects, James Wasmuth
    - Re: BLASTing BioSeq objects, Shawn
    - Re: BLASTing BioSeq objects, James Wasmuth
    - Re: BLASTing BioSeq objects, Jason Stajich
Problem with Bio::Annotation, Harry Wild
- Re: Problem with Bio::Annotation, Ewan Birney
- Revising the bioperl tutorial for release 1.2, Peter Schattner
- Re: Problem with Bio::Annotation, Jason Stajich
  - Re: Problem with Bio::Annotation, Harry Wild
- RE: Problem with Bio::Annotation, Hilmar Lapp
bond operator in genpept (follow-up), Alex Zelensky
- Re: bond operator in genpept (follow-up), Alex Zelensky
Smith Waterman and MPI, renata melo
- Re: Smith Waterman and MPI, Aaron J Mackey
Bio::Root::Root::new(), Heikki Lehvaslaiho
- Re: Bio::Root::Root::new(), Hilmar Lapp
  - Re: Re: Bio::Root::Root::new(), Heikki Lehvaslaiho
    - Re: Re: Bio::Root::Root::new(), Lincoln Stein
Creating Genbank file, Vilanova,David,LAUSANNE,NRC-BS
- Re: Creating Genbank file, Jason Stajich
Simple Align, remove columns, Shawn
- Re: Simple Align, remove columns, Ewan Birney
DNA Smith-Waterman?, Yee Man
- Re: DNA Smith-Waterman?, Ewan Birney
  - Re: DNA Smith-Waterman?, Yee Man
- RE: DNA Smith-Waterman?, nkuipers
ANN: O'Reilly's 2003 Bioinformatics Technology Conference, Harry Mangalam
- Re: ANN: O'Reilly's 2003 Bioinformatics Technology Conference, Harry Mangalam
Inhereting environmental variables, Andy Nunberg
- Re: Inhereting environmental variables, Jason Stajich
- Re: Inhereting environmental variables, david coornaert
Re: Merging exons in all transcripts for a gene, Jason Stajich
could not load phrap error, eicke felipe
- Re: could not load phrap error, Robson Francisco de Souza
- Re: could not load phrap error, Jason Stajich
  - Re: could not load phrap error, eicke felipe
    - Re: could not load phrap error, Jason Stajich
RE: NCBI eutils, NIH Email Delivery
Windows Testing, Paul Boutros
- Re: Windows Testing, Lincoln Stein
  - Re: Windows Testing, Ewan Birney
  - Re: Windows Testing, Paul Boutros
    - Re: Windows Testing, Lincoln Stein
- Re: Windows Testing, Paul Boutros
  - Re: Windows Testing, Ewan Birney
- Re: Windows Testing, Paul Boutros
  - Re: Windows Testing, Jason Stajich
    - Re: Windows Testing, Paul Boutros
RE: Pushing towards 1.2 -- simpleGOparser.t, Chris Zmasek
Re: speedbumps, Hilmar Lapp
Re: Not done with Bio::DB::Query [WAS: All done with Bio::DB::Query], Paul Boutros
- Re: Not done with Bio::DB::Query [WAS: All done with Bio::DB::Query], Lincoln Stein
- Re: Not done with Bio::DB::Query [WAS: All done with Bio::DB::Query], Lincoln Stein
  - Re: Not done with Bio::DB::Query [WAS: All done with Bio::DB::Query], Paul Boutros
ProtDist.pm, Tyler
- Re: ProtDist.pm, Jason Stajich
- Re: ProtDist.pm, Jason Stajich
HSP brain rot..., James Wasmuth
Re: All roads lead to Bio::Seq, Viren Konde
Re: Pushing towards 1.2, Ewan Birney
- Re: Pushing towards 1.2, Jason Stajich
- Re: Pushing towards 1.2, Hilmar Lapp
bug in location->to_FTstring, Philip Lijnzaad
- Re: bug in location->to_FTstring, Hilmar Lapp
  - Re: bug in location->to_FTstring, Philip Lijnzaad
    - Re: bug in location->to_FTstring, Jason Stajich
    - Re: bug in location->to_FTstring, Philip Lijnzaad
    - Re: bug in location->to_FTstring, Philip Lijnzaad
    - Re: bug in location->to_FTstring, Hilmar Lapp
    - Re: bug in location->to_FTstring, Hilmar Lapp