lang.perl.bio.general (date)

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lang.perl.bio.general (date)

December 31, 2003

Re: bioperl graphic question, Jason Stajich
Re: bioperl graphic question, Lincoln Stein
Environmental Energy Solutions, Sun Tracking & Flywheel Storage
Environmental Energy Solutions, Sun Tracking & Flywheel Storage
Re: my bioperl-db hacks, William Kenworthy

December 30, 2003

Re: my bioperl-db hacks, Hilmar Lapp
my bioperl-db hacks, T.D. Houfek
Re: Undefined subroutine &IO:String, Jason Stajich
Re: bioperl graphic question, Jason Stajich
Undefined subroutine &IO:String, Tim Stakenborg
Re: bioperl graphic question, Todd Harris
Re: bioperl graphic question, Lincoln Stein

December 29, 2003

bioperl graphic question, jun hu
bioperl graphic question, jun hu
Re: Alternate hit sorting for Bio::Search::Result objects, Donald Jackson

December 28, 2003

Re: Alternate hit sorting for Bio::Search::Result objects, Jason Stajich
Re: Alternate hit sorting for Bio::Search::Result objects, Chris Mungall

December 27, 2003

Re: some not-so-good perl practice in bioperl, Hilmar Lapp
Re: gapped translate, Jason Stajich
Re: gapped translate, Ewan Birney
gapped translate, Jason Stajich
Re: some not-so-good perl practice in bioperl, Ewan Birney
Re: Alternate hit sorting for Bio::Search::Result objects, Chris Mungall
Re: Getting CDS boundaries from Unflattener, Chris Mungall
Re: some not-so-good perl practice in bioperl, Chris Mungall

December 24, 2003

Re: wormbase115/Bio::DB::GFF::Aggregator wormbase_transcript problem, Lincoln Stein

December 23, 2003

Re: Alternate hit sorting for Bio::Search::Result objects, Jason Stajich
Alternate hit sorting for Bio::Search::Result objects, Donald G. Jackson
Fwd: Re: wormbase115/Bio::DB::GFF::Aggregator wormbase_transcript problem, Philip MacMenamin
Reminder to post 1.4 bioperl developers, Heikki Lehvaslaiho
Re: versioning, Aaron J. Mackey
Re: Really Minor (but annoying) things, Jason Stajich
Re: wormbase115/Bio::DB::GFF::Aggregator wormbase_transcript problem, Jason Stajich
wormbase115/Bio::DB::GFF::Aggregator wormbase_transcript problem, Philip MacMenamin
Re: versioning, Heikki Lehvaslaiho
substitution matrices, Andreas Bernauer
Re: versioning, Jason Stajich
Re: Bioperl Release 1.4, Lincoln Stein
Re: versioning, Ewan Birney
Re: Bioperl Release 1.4, Ewan Birney
versioning, Juguang Xiao
Re: Bioperl Release 1.4, Hilmar Lapp
Bioperl Release 1.4, Heikki Lehvaslaiho
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
Really Minor (but annoying) things, Rob Edwards

December 22, 2003

Re: some not-so-good perl practice in bioperl, Ewan Birney
Re: some not-so-good perl practice in bioperl, Hilmar Lapp
Re: some not-so-good perl practice in bioperl, Hilmar Lapp
Re: some not-so-good perl practice in bioperl, Lincoln Stein
Re: Question about Bio::TreeIO, Jason Stajich
Re: Bundle::Bioperl updated for bioperl-1.4 release, Heikki Lehvaslaiho
problems with Bio::Tools::BPbl2seq, Arye Shemesh
some not-so-good perl practice in bioperl, Juguang Xiao

December 21, 2003

Question about Bio::TreeIO, iain wallace
Re: [Bioperl-guts-l] [Bug 1573] New: Setting illegal ids, Heikki Lehvaslaiho

December 19, 2003

Re: Getting CDS boundaries from Unflattener, Scott Cain
Re: Getting CDS boundaries from Unflattener, Scott Cain
Mr. Uwe Schmidt is a knave! Don't buy any product from Microsale!, Microsale
Re: Bio::DB::Fasta, 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], Koen van der Drift

December 18, 2003

Bio::DB::Fasta, Eric Just
Re: Getting CDS boundaries from Unflattener, Chris Mungall
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
Bundle::Bioperl updated for bioperl-1.4 release, Chris Dagdigian
Getting CDS boundaries from Unflattener, Scott Cain
Re: Disabling web tests [some tests fail on Mac OS X], Heikki Lehvaslaiho
Re: AUTHORS, 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], Jason Stajich
Re: Disabling web tests [some tests fail on Mac OS X], Koen van der Drift

December 17, 2003

Bioperl Developer snapshot 1.3.04, Heikki Lehvaslaiho
AUTHORS, Jason Stajich
Re: Disabling web tests [some tests fail on Mac OS X], Jason Stajich
Re: bp_genbank2gff problems, Lincoln Stein
Re: bp_genbank2gff problems, Lincoln Stein
Re: Bug in SeqIO genbank output, Heikki Lehvaslaiho
Re: SeqIO tests fail, Heikki Lehvaslaiho
Re: Disabling web tests [some tests fail on Mac OS X], Heikki Lehvaslaiho
Re: How to proceed with 1.4?, Heikki Lehvaslaiho
SeqIO tests fail, Hilmar Lapp
Re: proposed additions to SeqFeatureI, RangeI and FeatureHolderI, Hilmar Lapp
Re: How to proceed with 1.4?, Hilmar Lapp
Re: Bio::Ontology::Term needs Bio::Annotation::Reference, Hilmar Lapp
Re: Bio::TreeIO, Rob Edwards

December 16, 2003

How can annotate a list of genes functionally using bioperl, omid gulban
full newick support (was Re: Root::IO handle Mac and Win32 LF), Jason Stajich
Re: Graphical alignments with blast, Steven Lembark
Re: Root::IO handle Mac and Win32 LF, Dave Howorth
Re: Root::IO handle Mac and Win32 LF, Allen Day
Re: Graphical alignments with blast, Jason Stajich
Re: Bio::TreeIO, Jason Stajich
Re: Trees as graphics, Allen Day
Graphical alignments with blast, Mike Muratet
Re: Root::IO handle Mac and Win32 LF, Jason Stajich
Re: Root::IO handle Mac and Win32 LF, Dave Howorth
Bio::TreeIO, Iain Wallace
Re: Root::IO handle Mac and Win32 LF, Jason Stajich
Re: some tests fail on Mac OS X, Heikki Lehvaslaiho
Trees as graphics, Nathan Haigh
Authenticating apache against LDAP, Simon, Deborah
Re: Root::IO handle Mac and Win32 LF, Aaron J. Mackey
Re: blast warning -- no valid letters to be indexed, Ian Korf
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
blast warning -- no valid letters to be indexed, Liu Haifeng
Bug in SeqIO genbank output, Wes Barris
Re: using graphics xyplot, Shawn Hoon
using graphics xyplot, Shawn Hoon
Re: repost the problem --- Re: bl2seq hang and itsperformace, Liu Haifeng
Re: some tests fail on Mac OS X, Koen van der Drift
Re: repost the problem --- Re: bl2seq hang and its performace, Jason Stajich
Re: some tests fail on Mac OS X, Jason Stajich
Re: some tests fail on Mac OS X, Koen van der Drift

December 15, 2003

game tests, Heikki Lehvaslaiho
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
Unflattener and GFF3 questions, Scott Cain
Root::IO handle Mac and Win32 LF, Jason Stajich
Re: some tests fail on Mac OS X, Jason Stajich
Re: [Bioperl-pipeline] biopipe/Pipeline Manager, Shawn Hoon
bp_genbank2gff problems, Neil Saunders
Re: Re: Changes to GFF 2.5 "unflattening" code, Scott Cain
Re: [Bioperl-guts-l] bioperl commit, Aaron J Mackey
Re: Bio::Restriction, Heikki Lehvaslaiho
biopipe/Pipeline Manager, matthieu CONTE
Re: Blast return codes, Matthew Laird
Re: some tests fail on Mac OS X, Rob Edwards
Bio::Restriction, Rob Edwards
Re: some tests fail on Mac OS X, Jason Stajich
repost the problem --- Re: bl2seq hang and its performace, Liu Haifeng

December 14, 2003

Re: some tests fail on Mac OS X, Koen van der Drift
Re: some tests fail on Mac OS X, Chris Dagdigian
Re: some tests fail on Mac OS X, Heikki Lehvaslaiho
Re: Blast return codes, Keith James
Re: some tests fail on Mac OS X, Koen van der Drift
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

December 13, 2003

Re: Experiences from a newbie, Andreas Bernauer
Re: some tests fail on Mac OS X, Jason Stajich
Re: some tests fail on Mac OS X, Rob Edwards
Re: some tests fail on Mac OS X, Koen van der Drift
Re: Bio::DB::GFF dna method not working for wormbase115., Philip E Macmenamin
Re: some tests fail on Mac OS X, Jason Stajich
Re: Experiences from a newbie, Jason Stajich
Re: Bio::MAGE, Adam Witney
Re: Bio::MAGE, Sebastian JÃ¼nemann
RE: Experiences from a newbie, Brian Osborne
some tests fail on Mac OS X, Koen van der Drift

December 12, 2003

Re: Question on whole-genome comparisions, Andreas Bernauer
Re: Experiences from a newbie, Andreas Bernauer
Re: Blast return codes, Matthew Laird
Re: Bio::DB::GFF dna method not working for wormbase115., Lincoln Stein
Re: Re: Changes to GFF 2.5 "unflattening" code, Chris Mungall
Re: using Bio::DB::GenBank get translation, Heikki Lehvaslaiho
RE: Question on whole-genome comparisions, Brian Osborne
Question on whole-genome comparisions, Steven Lembark
Bio::Graphics::Panel <DATA> section, Josh Lauricha
RE: Please help: upgraded to 1.2.3 and interfaces changed, Brian Osborne
Re: Changes to GFF 2.5 "unflattening" code, Scott Cain
RE: using Bio::DB::GenBank get translation, Brian Osborne
RE: using Bio::DB::GenBank get translation, Simon, Deborah
Re: using Bio::DB::GenBank get translation, Vince Forgetta
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, Jason Stajich
using Bio::DB::GenBank get translation, Vince Forgetta
Issues with Bio::Graphics resolved, Lincoln Stein
RE: Bio::Biblio, Brian Osborne
RE: Experiences from a newbie, Brian Osborne
RE: Experiences from a newbie, Brian Osborne
Re: Re: What happened to my dpAlign module?, Heikki Lehvaslaiho
bl2seq hang and its performace, Liu Haifeng
Re: [BioPerl] Re: here's a cool bug!, Mark Wilkinson
Re: here's a cool bug!, Jason Stajich
Re: Changes to GFF 2.5 "unflattening" code, Sheldon McKay
Changes to GFF 2.5 "unflattening" code, lstein
here's a cool bug!, Mark Wilkinson
Experiences from a newbie, andreas . bernauer

December 11, 2003

Re: Re: What happened to my dpAlign module?, Yee Man Chan
Re: Bio::DB::Fasta, Lincoln Stein
Re: Re: What happened to my dpAlign module?, Heikki Lehvaslaiho
Re: What happened to my dpAlign module?, Yee Man Chan
Re: Blast return codes, Matthew Laird
Re: [BioPerl] Bio::DB::GenBank (fwd), Mark Wilkinson
Re: problem using load_seqdatabase.pl with biosql, Hilmar Lapp
Bio::DB::Fasta, Jason Stajich
Re: [BioPerl] Bio::DB::GenBank (fwd), Jason Stajich
Re: [BioPerl] Bio::DB::GenBank (fwd), Mark Wilkinson
Re: [BioPerl] Bio::DB::GenBank (fwd), Heikki Lehvaslaiho
can't receive group emails, Alice Lu
Re: Bio::DB::GenBank (fwd), Heikki Lehvaslaiho
Re: [BioPerl] Bio::DB::GenBank (fwd), Mark Wilkinson
Bio::DB::GenBank (fwd), Jason Stajich
Re: Please help: upgraded to 1.2.3 and interfaces changed, Jason Stajich
RE: :structure, Jurgen Pletinckx
Problems in Bio::Graphics, lstein
updated bioperl Download page, Heikki Lehvaslaiho
Re: Blast return codes, Keith James
Re: Bio::Seq::RichSeq error, Heikki Lehvaslaiho
Bio::Seq::RichSeq error, Magic Fang
Please help: upgraded to 1.2.3 and interfaces changed, David Trusty
Bio::Biblio, Susan J. Miller
problem using load_seqdatabase.pl with biosql, John Yao

December 10, 2003

Bio::MAGE, Sebastian Jünemann
Re: Can Bio::SearchIO::psl.pm parse BlastZ output?, Feng Sun
Re: Bio::Tools::GuessSeqFormat unknown return value?, Heikki Lehvaslaiho
Re: Can Bio::SearchIO::psl.pm parse BlastZ output?, Wes Barris
Re: Can Bio::SearchIO::psl.pm parse BlastZ output?, Jason Stajich
Can Bio::SearchIO::psl.pm parse BlastZ output?, Feng Sun
RE: Bioperl parser for PolyPhred?, Cook, Malcolm
Re: Blast return codes, Matthew Laird
Re: Blast return codes, Keith James
Bio::DB::GFF dna method not working for wormbase115., Philip MacMenamin
RE: Blast return codes, Matthew Laird
Re: Bio::Tools::GuessSeqFormat unknown return value?, Hilmar Lapp
Re: Bio::Tools::GuessSeqFormat unknown return value?, Aaron J. Mackey
Bio::Ontology::Term needs Bio::Annotation::Reference, Juguang Xiao
Re: Bio::Tools::GuessSeqFormat unknown return value?, Andreas Kahari
Bio::Tools::GuessSeqFormat unknown return value?, Heikki Lehvaslaiho
Re: Bio::Restriction::Analysis feature merge, Peter Blaiklock
Re: Problem with Unflattener, Scott Cain
Re: Problem with Unflattener, Chris Mungall
Re: Problem with Unflattener, Scott Cain
Re: Problem with Unflattener, Chris Mungall

December 09, 2003

Re: Bio::Restriction::Analysis feature merge, Rob Edwards
RE: How to proceed with 1.4?, Brian Osborne
Re: RNA fold, Chris Fields
Problem with Unflattener, Scott Cain
Re: RNA fold, Sam Griffiths-Jones
Re: RNA fold, Chris Fields
Re: How to proceed with 1.4?, Ewan Birney
Re: RNA fold, Chris Fields
Re: RNA fold, Jason Stajich
Re: RNA fold, Stephen Baird
Re: How to proceed with 1.4?, Ewan Birney
How to proceed with 1.4?, Heikki Lehvaslaiho
RE: Blast return codes, Joseph Bedell
Re: Loading SwissProt Data into Oracle, Hilmar Lapp

December 08, 2003

Re: Bioperl parser for PolyPhred?, Jason Stajich
Re: Bioperl parser for PolyPhred?, Yee Man Chan
Bioperl-ext Developer snapshot 1.3.01, Heikki Lehvaslaiho
Re: Bioperl parser for PolyPhred?, Christopher Milton
Re: RNA fold, Chris Fields
Bioperl-run Developer snapshot 1.3.01, Heikki Lehvaslaiho
Bioperl parser for PolyPhred?, Yee Man Chan
Re: RNA fold, Jason Stajich
Re: Getting a Gene Object, Ewan Birney
Re: Getting a Gene Object, Jason Stajich
Getting a Gene Object, James Wasmuth
Re: Re: I want to construct BioC#. Can you help me?, Phillip Lord
Re: I want to construct BioC#. Can you help me?, Heikki Lehvaslaiho
Bio::Restriction::Analysis feature merge, Peter Blaiklock

December 07, 2003

indexing nr database, Sanjib Dutta
Re: RNA fold, Chris Fields

December 06, 2003

RE: RNA fold, Morten Lindow
Re: RNA fold, Catherine Letondal

December 05, 2003

Re: RNA fold, Jason Stajich
Re: RNA fold, Allen Day
Blast return codes, Matthew Laird
RNA fold, Vesko Baev
Loading SwissProt Data into Oracle, kyliu

December 04, 2003

Interpro parser example, Juguang Xiao
Re: change in Tools::SeqWords not reflected in tutorial link, Derek Gatherer
Re: Re: [Bioperl-guts-l] Bio::Restriction modifications, Peter Blaiklock

December 03, 2003

RE: change in Tools::SeqWords not reflected in tutorial link, Brian Osborne
Re: proposed additions to SeqFeatureI, RangeI and FeatureHolderI, Chris Mungall
change in Tools::SeqWords not reflected in tutorial link, William Hsiao
Re: Sorting Bio:Graphics::Glyphs, Oliver Burren
Re: Sorting Bio:Graphics::Glyphs, Lincoln Stein
Sorting Bio:Graphics::Glyphs, Oliver Burren
Re: Graphics:Panel /SeqFeature::Generic, Lincoln Stein
Re: [Bioperl-guts-l] Bio::Restriction modifications, Rob Edwards
Re: [Bioperl-guts-l] Bio::Restriction modifications, Heikki Lehvaslaiho
Re: Graphics:Panel /SeqFeature::Generic, Daniel Lang
Re: Graphics:Panel /SeqFeature::Generic, Lincoln Stein
ComAlign, Terry

December 02, 2003

Re: Re: [Bioperl-guts-l] bioperl commit, Aaron J. Mackey
Re: Re: What happened to my dpAlign module?, Heikki Lehvaslaiho
Re: Re: [Bioperl-guts-l] bioperl commit, Heikki Lehvaslaiho
Re: [Bioperl-guts-l] bioperl commit, Aaron J. Mackey
Re: Graphics:Panel /SeqFeature::Generic, Lincoln Stein
Re: GFF file output missing semicolon, Lincoln Stein
RE: parser genbank, Brian Osborne
Re: [DAS] ProServer, a pluggable DAS server, Bio::SeqIO support added, Lincoln Stein
parser genbank, Fabiola Sánchez
Re: What happened to my dpAlign module?, Heikki Lehvaslaiho
guessing sequence format, Heikki Lehvaslaiho
Error: 5X35#42 Mail delivery problem, Postmaster
RE: running remoteblast, Wiepert, Mathieu
Re: running remoteblast, Jason Stajich

December 01, 2003

running remoteblast, omid gulban

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