lang.perl.bio.general (thread)

Environmental Energy Solutions, Sun Tracking & Flywheel Storage
- Environmental Energy Solutions, Sun Tracking & Flywheel Storage
my bioperl-db hacks, T.D. Houfek
- Re: my bioperl-db hacks, Hilmar Lapp
  - Re: my bioperl-db hacks, William Kenworthy
Undefined subroutine &IO:String, Tim Stakenborg
- Re: Undefined subroutine &IO:String, Jason Stajich
bioperl graphic question, jun hu
- bioperl graphic question, jun hu
  - Re: bioperl graphic question, Lincoln Stein
  - Re: bioperl graphic question, Todd Harris
    - Re: bioperl graphic question, Jason Stajich
    - Re: bioperl graphic question, Lincoln Stein
    - Re: bioperl graphic question, Jason Stajich
gapped translate, Jason Stajich
- Re: gapped translate, Ewan Birney
  - Re: gapped translate, Jason Stajich
Alternate hit sorting for Bio::Search::Result objects, Donald G. Jackson
- Re: Alternate hit sorting for Bio::Search::Result objects, Jason Stajich
  - Re: Alternate hit sorting for Bio::Search::Result objects, Chris Mungall
    - Re: Alternate hit sorting for Bio::Search::Result objects, Chris Mungall
    - Re: Alternate hit sorting for Bio::Search::Result objects, Jason Stajich
- Re: Alternate hit sorting for Bio::Search::Result objects, Donald Jackson
Reminder to post 1.4 bioperl developers, Heikki Lehvaslaiho
wormbase115/Bio::DB::GFF::Aggregator wormbase_transcript problem, Philip MacMenamin
- Re: wormbase115/Bio::DB::GFF::Aggregator wormbase_transcript problem, Jason Stajich
- Re: wormbase115/Bio::DB::GFF::Aggregator wormbase_transcript problem, Lincoln Stein
- Fwd: Re: wormbase115/Bio::DB::GFF::Aggregator wormbase_transcript problem, Philip MacMenamin
substitution matrices, Andreas Bernauer
versioning, Juguang Xiao
- Re: versioning, Ewan Birney
- Re: versioning, Jason Stajich
- Re: versioning, Heikki Lehvaslaiho
  - Re: versioning, Aaron J. Mackey
Bioperl Release 1.4, Heikki Lehvaslaiho
- Re: Bioperl Release 1.4, Hilmar Lapp
- Re: Bioperl Release 1.4, Ewan Birney
  - Re: Bioperl Release 1.4, Lincoln Stein
Really Minor (but annoying) things, Rob Edwards
- Re: Really Minor (but annoying) things, Jason Stajich
problems with Bio::Tools::BPbl2seq, Arye Shemesh
some not-so-good perl practice in bioperl, Juguang Xiao
- Re: some not-so-good perl practice in bioperl, Lincoln Stein
  - Re: some not-so-good perl practice in bioperl, Hilmar Lapp
    - Re: some not-so-good perl practice in bioperl, Juguang Xiao
    - Re: some not-so-good perl practice in bioperl, Hilmar Lapp
    - Re: some not-so-good perl practice in bioperl, Juguang Xiao
  - Re: some not-so-good perl practice in bioperl, Juguang Xiao
- Re: some not-so-good perl practice in bioperl, Hilmar Lapp
  - Re: some not-so-good perl practice in bioperl, Ewan Birney
    - Re: some not-so-good perl practice in bioperl, Chris Mungall
    - Re: some not-so-good perl practice in bioperl, Ewan Birney
    - Re: some not-so-good perl practice in bioperl, Hilmar Lapp
Question about Bio::TreeIO, iain wallace
- Re: Question about Bio::TreeIO, Jason Stajich
Re: [Bioperl-guts-l] [Bug 1573] New: Setting illegal ids, Heikki Lehvaslaiho
Mr. Uwe Schmidt is a knave! Don't buy any product from Microsale!, Microsale
Bundle::Bioperl updated for bioperl-1.4 release, Chris Dagdigian
- Re: Bundle::Bioperl updated for bioperl-1.4 release, Allen Day
  - Re: Bundle::Bioperl updated for bioperl-1.4 release, Heikki Lehvaslaiho
    - Re: Bundle::Bioperl updated for bioperl-1.4 release, Allen Day
- Re: Bundle::Bioperl updated for bioperl-1.4 release, Heikki Lehvaslaiho
Getting CDS boundaries from Unflattener, Scott Cain
- Re: Getting CDS boundaries from Unflattener, Chris Mungall
  - Re: Getting CDS boundaries from Unflattener, Scott Cain
    - Re: Getting CDS boundaries from Unflattener, Scott Cain
    - Re: Getting CDS boundaries from Unflattener, Chris Mungall
Bioperl Developer snapshot 1.3.04, Heikki Lehvaslaiho
AUTHORS, Jason Stajich
- Re: AUTHORS, Heikki Lehvaslaiho
SeqIO tests fail, Hilmar Lapp
- Re: SeqIO tests fail, Heikki Lehvaslaiho
How can annotate a list of genes functionally using bioperl, omid gulban
Graphical alignments with blast, Mike Muratet
- Re: Graphical alignments with blast, Jason Stajich
  - Re: Graphical alignments with blast, Steven Lembark
Bio::TreeIO, Iain Wallace
- Re: Bio::TreeIO, Jason Stajich
- Re: Bio::TreeIO, Rob Edwards
Trees as graphics, Nathan Haigh
- Re: Trees as graphics, Allen Day
Authenticating apache against LDAP, Simon, Deborah
blast warning -- no valid letters to be indexed, Liu Haifeng
- Re: blast warning -- no valid letters to be indexed, Ian Korf
Bug in SeqIO genbank output, Wes Barris
- Re: Bug in SeqIO genbank output, Heikki Lehvaslaiho
using graphics xyplot, Shawn Hoon
- Re: using graphics xyplot, Shawn Hoon
game tests, Heikki Lehvaslaiho
Unflattener and GFF3 questions, Scott Cain
Root::IO handle Mac and Win32 LF, Jason Stajich
- Re: Root::IO handle Mac and Win32 LF, Allen Day
- Re: Root::IO handle Mac and Win32 LF, Aaron J. Mackey
  - Re: Root::IO handle Mac and Win32 LF, Allen Day
    - Re: Root::IO handle Mac and Win32 LF, Dave Howorth
    - Re: Root::IO handle Mac and Win32 LF, Aaron J. Mackey
    - Re: Root::IO handle Mac and Win32 LF, Dave Howorth
    - Re: Root::IO handle Mac and Win32 LF, Aaron J. Mackey
    - Re: Root::IO handle Mac and Win32 LF, Jason Stajich
    - Re: Root::IO handle Mac and Win32 LF, Dave Howorth
    - Re: Root::IO handle Mac and Win32 LF, Jason Stajich
    - Re: Root::IO handle Mac and Win32 LF, Allen Day
    - Re: Root::IO handle Mac and Win32 LF, Dave Howorth
    - full newick support (was Re: Root::IO handle Mac and Win32 LF), Jason Stajich
bp_genbank2gff problems, Neil Saunders
- Message not available
  - Message not available
    - Re: bp_genbank2gff problems, Lincoln Stein
- Re: bp_genbank2gff problems, Lincoln Stein
biopipe/Pipeline Manager, matthieu CONTE
- Re: [Bioperl-pipeline] biopipe/Pipeline Manager, Shawn Hoon
Bio::Restriction, Rob Edwards
- Re: Bio::Restriction, Heikki Lehvaslaiho
repost the problem --- Re: bl2seq hang and its performace, Liu Haifeng
- Re: repost the problem --- Re: bl2seq hang and its performace, Jason Stajich
  - Re: repost the problem --- Re: bl2seq hang and itsperformace, Liu Haifeng
some tests fail on Mac OS X, Koen van der Drift
- Re: some tests fail on Mac OS X, Jason Stajich
  - Re: some tests fail on Mac OS X, Koen van der Drift
    - Re: some tests fail on Mac OS X, Jason Stajich
    - Re: some tests fail on Mac OS X, Koen van der Drift
    - Re: some tests fail on Mac OS X, Jason Stajich
    - Re: some tests fail on Mac OS X, Koen van der Drift
    - Re: some tests fail on Mac OS X, Heikki Lehvaslaiho
    - Re: some tests fail on Mac OS X, Chris Dagdigian
    - Re: some tests fail on Mac OS X, Koen van der Drift
    - Re: some tests fail on Mac OS X, Jason Stajich
    - Re: some tests fail on Mac OS X, Koen van der Drift
    - Re: some tests fail on Mac OS X, Jason Stajich
    - Re: some tests fail on Mac OS X, Koen van der Drift
    - Re: some tests fail on Mac OS X, Heikki Lehvaslaiho
    - Re: Disabling web tests [some tests fail on Mac OS X], Heikki Lehvaslaiho
    - Re: Disabling web tests [some tests fail on Mac OS X], Jason Stajich
    - Re: Disabling web tests [some tests fail on Mac OS X], Koen van der Drift
    - Re: Disabling web tests [some tests fail on Mac OS X], Jason Stajich
    - Re: Disabling web tests [some tests fail on Mac OS X], Koen van der Drift
    - Re: Disabling web tests [some tests fail on Mac OS X], Heikki Lehvaslaiho
    - Re: Disabling web tests [some tests fail on Mac OS X], Koen van der Drift
    - Re: Disabling web tests [some tests fail on Mac OS X], Heikki Lehvaslaiho
    - Re: some tests fail on Mac OS X, Rob Edwards
    - Re: some tests fail on Mac OS X, Jason Stajich
  - Re: some tests fail on Mac OS X, Koen van der Drift
- Re: some tests fail on Mac OS X, Rob Edwards
Question on whole-genome comparisions, Steven Lembark
- RE: Question on whole-genome comparisions, Brian Osborne
- Re: Question on whole-genome comparisions, Andreas Bernauer
Bio::Graphics::Panel <DATA> section, Josh Lauricha
using Bio::DB::GenBank get translation, Vince Forgetta
- Re: using Bio::DB::GenBank get translation, Jason Stajich
  - Re: using Bio::DB::GenBank get translation, Vince Forgetta
- RE: using Bio::DB::GenBank get translation, Brian Osborne
  - Re: using Bio::DB::GenBank get translation, Vince Forgetta
    - RE: using Bio::DB::GenBank get translation, Brian Osborne
  - Re: using Bio::DB::GenBank get translation, Vince Forgetta
- Re: using Bio::DB::GenBank get translation, Heikki Lehvaslaiho
- RE: using Bio::DB::GenBank get translation, Simon, Deborah
Issues with Bio::Graphics resolved, Lincoln Stein
bl2seq hang and its performace, Liu Haifeng
Changes to GFF 2.5 "unflattening" code, lstein
- Re: Changes to GFF 2.5 "unflattening" code, Sheldon McKay
- Re: Changes to GFF 2.5 "unflattening" code, Scott Cain
  - Re: Re: Changes to GFF 2.5 "unflattening" code, Chris Mungall
    - Re: Re: Changes to GFF 2.5 "unflattening" code, Scott Cain
Experiences from a newbie, andreas . bernauer
- RE: Experiences from a newbie, Brian Osborne
  - RE: Experiences from a newbie, Brian Osborne
    - Re: Experiences from a newbie, Andreas Bernauer
    - RE: Experiences from a newbie, Brian Osborne
    - Re: Experiences from a newbie, Jason Stajich
    - Re: Experiences from a newbie, Andreas Bernauer
Bio::DB::Fasta, Jason Stajich
- Re: Bio::DB::Fasta, Lincoln Stein
- here's a cool bug!, Mark Wilkinson
  - Re: here's a cool bug!, Jason Stajich
    - Re: [BioPerl] Re: here's a cool bug!, Mark Wilkinson
- Bio::DB::Fasta, Eric Just
  - Re: Bio::DB::Fasta, Heikki Lehvaslaiho
can't receive group emails, Alice Lu
Bio::DB::GenBank (fwd), Jason Stajich
- Re: [BioPerl] Bio::DB::GenBank (fwd), Mark Wilkinson
  - Re: [BioPerl] Bio::DB::GenBank (fwd), Heikki Lehvaslaiho
    - Re: [BioPerl] Bio::DB::GenBank (fwd), Mark Wilkinson
  - Re: [BioPerl] Bio::DB::GenBank (fwd), Jason Stajich
    - Re: [BioPerl] Bio::DB::GenBank (fwd), Mark Wilkinson
- Re: Bio::DB::GenBank (fwd), Heikki Lehvaslaiho
RE: :structure, Jurgen Pletinckx
Problems in Bio::Graphics, lstein
updated bioperl Download page, Heikki Lehvaslaiho
Bio::Seq::RichSeq error, Magic Fang
- Re: Bio::Seq::RichSeq error, Heikki Lehvaslaiho
Please help: upgraded to 1.2.3 and interfaces changed, David Trusty
- Re: Please help: upgraded to 1.2.3 and interfaces changed, Jason Stajich
- RE: Please help: upgraded to 1.2.3 and interfaces changed, Brian Osborne
Bio::Biblio, Susan J. Miller
- RE: Bio::Biblio, Brian Osborne
problem using load_seqdatabase.pl with biosql, John Yao
- Re: problem using load_seqdatabase.pl with biosql, Hilmar Lapp
Bio::MAGE, Sebastian Jünemann
- Re: Bio::MAGE, Sebastian JÃ¼nemann
  - Re: Bio::MAGE, Adam Witney
Can Bio::SearchIO::psl.pm parse BlastZ output?, Feng Sun
- Re: Can Bio::SearchIO::psl.pm parse BlastZ output?, Jason Stajich
  - Re: Can Bio::SearchIO::psl.pm parse BlastZ output?, Feng Sun
- Re: Can Bio::SearchIO::psl.pm parse BlastZ output?, Wes Barris
Bio::DB::GFF dna method not working for wormbase115., Philip MacMenamin
- Re: Bio::DB::GFF dna method not working for wormbase115., Lincoln Stein
- Re: Bio::DB::GFF dna method not working for wormbase115., Philip E Macmenamin
Bio::Ontology::Term needs Bio::Annotation::Reference, Juguang Xiao
- Re: Bio::Ontology::Term needs Bio::Annotation::Reference, Hilmar Lapp
Bio::Tools::GuessSeqFormat unknown return value?, Heikki Lehvaslaiho
- Re: Bio::Tools::GuessSeqFormat unknown return value?, Andreas Kahari
- Re: Bio::Tools::GuessSeqFormat unknown return value?, Aaron J. Mackey
  - Re: Bio::Tools::GuessSeqFormat unknown return value?, Hilmar Lapp
    - Re: Bio::Tools::GuessSeqFormat unknown return value?, Heikki Lehvaslaiho
Problem with Unflattener, Scott Cain
- Re: Problem with Unflattener, Chris Mungall
  - Re: Problem with Unflattener, Scott Cain
    - Re: Problem with Unflattener, Chris Mungall
    - Re: Problem with Unflattener, Scott Cain
How to proceed with 1.4?, Heikki Lehvaslaiho
- Re: How to proceed with 1.4?, Ewan Birney
- Re: How to proceed with 1.4?, Ewan Birney
- RE: How to proceed with 1.4?, Brian Osborne
- Re: How to proceed with 1.4?, Hilmar Lapp
  - Re: How to proceed with 1.4?, Heikki Lehvaslaiho
Bioperl-ext Developer snapshot 1.3.01, Heikki Lehvaslaiho
Bioperl-run Developer snapshot 1.3.01, Heikki Lehvaslaiho
Bioperl parser for PolyPhred?, Yee Man Chan
- Re: Bioperl parser for PolyPhred?, Christopher Milton
  - Re: Bioperl parser for PolyPhred?, Yee Man Chan
    - Re: Bioperl parser for PolyPhred?, Jason Stajich
- RE: Bioperl parser for PolyPhred?, Cook, Malcolm
Getting a Gene Object, James Wasmuth
- Re: Getting a Gene Object, Jason Stajich
- Re: Getting a Gene Object, Ewan Birney
Re: I want to construct BioC#. Can you help me?, Heikki Lehvaslaiho
- Re: Re: I want to construct BioC#. Can you help me?, Phillip Lord
Bio::Restriction::Analysis feature merge, Peter Blaiklock
- Re: Bio::Restriction::Analysis feature merge, Rob Edwards
  - Re: Bio::Restriction::Analysis feature merge, Peter Blaiklock
indexing nr database, Sanjib Dutta
Blast return codes, Matthew Laird
- RE: Blast return codes, Joseph Bedell
  - RE: Blast return codes, Matthew Laird
    - Re: Blast return codes, Keith James
    - Re: Blast return codes, Matthew Laird
    - Re: Blast return codes, Keith James
    - Re: Blast return codes, Matthew Laird
    - Re: Blast return codes, Matthew Laird
    - Re: Blast return codes, Keith James
    - Re: Blast return codes, Matthew Laird
RNA fold, Vesko Baev
- Re: RNA fold, Allen Day
- Re: RNA fold, Jason Stajich
- Re: RNA fold, Catherine Letondal
  - RE: RNA fold, Morten Lindow
- Re: RNA fold, Chris Fields
  - Re: RNA fold, Jason Stajich
    - Re: RNA fold, Chris Fields
    - Re: RNA fold, Stephen Baird
    - Re: RNA fold, Jason Stajich
    - Re: RNA fold, Chris Fields
    - Re: RNA fold, Chris Fields
    - Re: RNA fold, Sam Griffiths-Jones
    - Re: RNA fold, Chris Fields
Loading SwissProt Data into Oracle, kyliu
- Re: Loading SwissProt Data into Oracle, Hilmar Lapp
Interpro parser example, Juguang Xiao
Re: change in Tools::SeqWords not reflected in tutorial link, Derek Gatherer
Re: proposed additions to SeqFeatureI, RangeI and FeatureHolderI, Chris Mungall
- Re: proposed additions to SeqFeatureI, RangeI and FeatureHolderI, Hilmar Lapp
change in Tools::SeqWords not reflected in tutorial link, William Hsiao
- RE: change in Tools::SeqWords not reflected in tutorial link, Brian Osborne
Sorting Bio:Graphics::Glyphs, Oliver Burren
- Re: Sorting Bio:Graphics::Glyphs, Lincoln Stein
  - Re: Sorting Bio:Graphics::Glyphs, Oliver Burren
Re: [Bioperl-guts-l] Bio::Restriction modifications, Heikki Lehvaslaiho
- Re: [Bioperl-guts-l] Bio::Restriction modifications, Rob Edwards
  - Re: Re: [Bioperl-guts-l] Bio::Restriction modifications, Peter Blaiklock
ComAlign, Terry
Re: [Bioperl-guts-l] bioperl commit, Aaron J. Mackey
- Re: Re: [Bioperl-guts-l] bioperl commit, Heikki Lehvaslaiho
  - Re: Re: [Bioperl-guts-l] bioperl commit, Aaron J. Mackey
- Re: [Bioperl-guts-l] bioperl commit, Aaron J Mackey
Re: Graphics:Panel /SeqFeature::Generic, Lincoln Stein
- Re: Graphics:Panel /SeqFeature::Generic, Lincoln Stein
  - Re: Graphics:Panel /SeqFeature::Generic, Daniel Lang
    - Re: Graphics:Panel /SeqFeature::Generic, Lincoln Stein
Re: GFF file output missing semicolon, Lincoln Stein
Re: [DAS] ProServer, a pluggable DAS server, Bio::SeqIO support added, Lincoln Stein
parser genbank, Fabiola Sánchez
- RE: parser genbank, Brian Osborne
Re: What happened to my dpAlign module?, Heikki Lehvaslaiho
- Message not available
  - Re: Re: What happened to my dpAlign module?, Heikki Lehvaslaiho
- Re: What happened to my dpAlign module?, Yee Man Chan
  - Re: Re: What happened to my dpAlign module?, Heikki Lehvaslaiho
    - Re: Re: What happened to my dpAlign module?, Yee Man Chan
    - Re: Re: What happened to my dpAlign module?, Heikki Lehvaslaiho
guessing sequence format, Heikki Lehvaslaiho
Error: 5X35#42 Mail delivery problem, Postmaster
running remoteblast, omid gulban
- Re: running remoteblast, Jason Stajich
- RE: running remoteblast, Wiepert, Mathieu