lang.perl.bio.general (date)

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lang.perl.bio.general (date)

May 31, 2003

One more odd little parsing problem for your list, Michael Muratet
Re: passing multiple databases to blastall, James Wasmuth
Where to get BLASTCLUST or equivalent?, Cyril C.C. Chua
bioperl-run 1.2.0 tarball available, Shawn Hoon
problems by installing bioperl, Karine Prat

May 30, 2003

passing multiple databases to blastall, Andrew Nunberg
How can I edit a sequence?, Yee Man Chan
Changing extent of Bio::Graphics::Panel, Benjamin Berman
Re: Bio::Structure with CGI!, Jason Stajich

May 29, 2003

virtual gel from chromatogram, staden library on Windows, Sebastien Letort
RE: can't remember if I mentioned it..., Brian Osborne
bioperl-run 1.2.0 release, Shawn Hoon
Re: Bio::Structure with CGI!, Heikki Lehvaslaiho
Bio::Structure with CGI!, UT

May 28, 2003

TIGR XML IO, Josh Lauricha
can't remember if I mentioned it..., Ewan Birney
first pass at interactive script installation, Lincoln Stein
Re: Re: Another update for my alignment module, Yee Man Chan
Re: parse cds and peptide from genbank file with identifier, Jason Stajich
Unsubscription, Felipe Faco
modules for siRNA design, Donald Jackson
RE: New feature "Bond", Heikki Lehvaslaiho
Re: [BioSQL-l] Proposal on Bio::DB::BioSQL::MultiDB, Hilmar Lapp
Re: [BioSQL-l] How to find by foreign key?, Hilmar Lapp
bioperl-db: small change to create() instruction flow, Hilmar Lapp
ontology loader, Hilmar Lapp
parse cds and peptide from genbank file with identifier, Guoqi4
Re: Game XML writer/parser, Sheldon McKay
Re: Strand direction in Bl2seq, Jason Stajich

May 27, 2003

Strand direction in Bl2seq, Julio Fernandez Banet
Re: RE: New feature "Bond", tex
Re: avantgo-friendly web page with list archives, Hilmar Lapp
avantgo-friendly web page with list archives, Jonathan Epstein
Unsubscribtion, Felipe Faco
Updated Apache disables GBrowse, clangin
Updated Apache disables GBrowse, clangin
RE: tuning load_seqdatabase.db script in bioperl-db, Hilmar Lapp
RE: New feature "Bond", Hilmar Lapp
RE: tuning load_seqdatabase.db script in bioperl-db, Hilmar Lapp
Re: Bio::Graphics (circular map), Lincoln Stein
Re: SearchIO, last hit in blast report dropped, Jason Stajich
Re: New feature "Bond", Lincoln Stein
Re: New feature "Bond", Jason Stajich
Re: SearchIO, last hit in blast report dropped, Jason Stajich
New feature "Bond", M K. Govind

May 26, 2003

Re: tuning load_seqdatabase.db script in bioperl-db, Ewan Birney
tuning load_seqdatabase.db script in bioperl-db, Nicolas Rueff
Re: Re: Analysis Tests, shawn hoon

May 25, 2003

Re: Analysis Tests, Martin Senger
Re: TermI::get_dblinks inconsistent?, Ewan Birney
Re: ermI::get_dblinks inconsistent?, Michal Kurowski
Re: operating systems and bio-computing, Steven Lembark
Analysis Tests, Shawn Hoon
TermI::get_dblinks inconsistent?, Hilmar Lapp

May 24, 2003

Re: SearchIO, last hit in blast report dropped, Hilmar Lapp
Re: exonerate (cigar line) to GFF, Jason Stajich
Re: SearchIO, last hit in blast report dropped, Jason Stajich
SearchIO, last hit in blast report dropped, claus vogl

May 23, 2003

bioperl-db: don't just add exceptions please, Hilmar Lapp
GlimmerM parser, Jason Stajich
Re: Test DB.t fails, Jason Stajich
Test DB.t fails, Hilmar Lapp
Re: BioSQL and Bioperl-db inching towards release, Allen Day
Re: BioSQL and Bioperl-db inching towards release, Jason Stajich
Re: BioSQL and Bioperl-db inching towards release, Jason Stajich
Re: BioSQL and Bioperl-db inching towards release, Hilmar Lapp
Re: BioSQL and Bioperl-db inching towards release, Jason Stajich
BioSQL and Bioperl-db inching towards release, Hilmar Lapp
OBDA/Flat question, Brian Osborne
Re: Trying to use Bio::Graphics, Vikas Daga

May 22, 2003

RE: Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Hilmar Lapp
exonerate (cigar line) to GFF, Charles Hauser
Re: Trying to use Bio::Graphics, Lincoln Stein
RE: Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Brian Osborne
Re: Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Lincoln Stein
Re: Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Lincoln Stein
Re: Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Lincoln Stein
RE: Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Brian Osborne
RE: Repeat element check, Brian Osborne
Re: Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Ewan Birney
RE: Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Brian Osborne
Re: Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Andreas Kahari
Repeat element check, M K. Govind
Why is '+' a delimiter in $OBDA_SEARCH_PATH?, Brian Osborne
Re: Re: Another update for my alignment module, Yee Man Chan
Trying to use Bio::Graphics, Vikas Daga
Re: Re: Another update for my alignment module, Yee Man Chan

May 21, 2003

Re: Re: Another update for my alignment module, Yee Man Chan
Re: querying LocusLink, Hilmar Lapp
Re: add identifier to Bio::Seq object returned by fetch(), Jason Stajich
add identifier to Bio::Seq object returned by fetch(), Prachi Shah
Re: Re: Another update for my alignment module, Aaron J Mackey
RE: loading bioSQL schemas, Jason Stajich
RE: loading bioSQL schemas, Steve Mathias
RE: loading bioSQL schemas, Hilmar Lapp
loading bioSQL schemas, ulrik plate
Re: Re: Another update for my alignment module, Yee Man Chan
Re: Re: Another update for my alignment module, Aaron J Mackey
Re: runnable SYNOPSIS + general Analysis client added, Catherine Letondal

May 20, 2003

Re: bioperl and Perl, Bob Freeman
Re: bioperl and Perl, Jason Stajich
Re: Re: Another update for my alignment module, Yee Man Chan
ISMB/BOSC roll-call -- bioperl speaker needed, Chris Dagdigian
Re: Bioperl-l Digest, Vol 1, Issue 25 (Eric E. Snyder: incommunicado), Eric Snyder
Re: Re: Another update for my alignment module, Aaron J Mackey
Re: bioperl and Perl, Jason Stajich
bioperl and Perl, Line Neil
Re: Another update for my alignment module, Ewan Birney
Root::IO tempfile error, kaboroev

May 19, 2003

Another update for my alignment module, Yee Man Chan
RE: tests failing miserably, Jason Stajich
Re: Re: should Bio::PrimarySeq be storage-independent after bioperl-db appear?, Hilmar Lapp
Re: Re: should Bio::PrimarySeq be storage-independent after bioperl-db appear?, Juguang Xiao

May 18, 2003

Re: runnable SYNOPSIS, Ewan Birney

May 17, 2003

Re: Some problems about Bioperl-sql database structure, Hilmar Lapp
Re: Locuslink?? Help, Hilmar Lapp
Re: runnable SYNOPSIS, Hilmar Lapp
runnable SYNOPSIS, Heikki Lehvaslaiho

May 16, 2003

LocusLink Help, Eric Wang
Re: Factory::GenericObjectFactory, Steve Chervitz
commits coming in, Jason Stajich
Re: should Bio::PrimarySeq be storage-independent after bioperl-db appear?, Hilmar Lapp
Re: pub.open-bio.org down?, Chris Dagdigian
pub.open-bio.org down?, Lincoln Stein
RE: Blast Output, Leonardo Marino-Ramirez
Re: Blast Output, Andreas Kahari
Blast Output, Andreas Bernthaler

May 15, 2003

Re: bioperl on MacOS X... a beginner's problems..., Hilmar Lapp
Re: bioperl on MacOS X... a beginner's problems..., Chris Dagdigian
Re: Locuslink?? Help, Eric Wang
Re: bioperl on MacOS X... a beginner's problems..., Jason Stajich
Re: Can Bio::Graphics render a muti_segments picture?, Lincoln Stein
RE: tests failing miserably, Hilmar Lapp
Re: bioperl on MacOS X... a beginner's problems..., Thomas Keller
Re: bioperl on MacOS X... a beginner's problems..., Jason Stajich
Sir Laugh-a-lot, Phone Pranks
Re: Can Bio::Graphics render a muti_segments picture?, Lincoln Stein
bioperl on MacOS X... a beginner's problems..., Stefanie
moving bioperl/biodas website and mailing lists to a new server; possible email delays this weekend, Chris Dagdigian
Re: POD GOD, Heikki Lehvaslaiho
(no subject), Sally Li
POD GOD, Jason Stajich
Re: tests failing miserably, Jason Stajich
Re: tests failing miserably, Jason Stajich
Re: tests failing miserably, Heikki Lehvaslaiho
Re: tests failing miserably, Hilmar Lapp
Factory::GenericObjectFactory, Hilmar Lapp
Re: tests failing miserably, Hilmar Lapp
Re: Locuslink?? Help, Eric Wang
Re: Locuslink?? Help, Hilmar Lapp
Re: tests failing miserably, Hilmar Lapp
RE: Can Bio::Graphics render a muti_segments picture?, tongw
Locuslink?? Help, Eric Wang

May 14, 2003

Re: tests failing miserably, Hilmar Lapp
tests failing miserably, Hilmar Lapp
Re: Can Bio::Graphics render a muti_segments picture?, Lincoln Stein
Re: operating systems and bio-computing, Mark Dalphin
Re: operating systems and bio-computing, Chris Dagdigian
operating systems and bio-computing, Thomas Keller
RE: Can Bio::Graphics render a muti_segments picture?, tongw

May 13, 2003

Re: Can Bio::Graphics render a muti_segments picture?, Lincoln Stein
SearchIO parsing of RPS-BLAST misses last hit within each result?, M L
Re: SearchIO parsing of RPS-BLAST misses last hit within each result?, M L
Re: wuBlast, Jason Stajich
Re: SearchIO parsing of RPS-BLAST misses last hit within each result?, Jason Stajich
Re: Game XML writer/parser, Jason Stajich
Some problems about Bioperl-sql database structure, Nicolas Rueff
wuBlast, Josh Lauricha
Game XML writer/parser, Eileen Ying Wang
RE: Can Bio::Graphics render a muti_segments picture?, tongw

May 12, 2003

Re: Scale with Bio::Grahics for upstream regions, Lincoln Stein
SearchIO parsing of RPS-BLAST misses last hit within each result?, M L
Re: directory for bioperl maintenance scripts, Ewan Birney
RE: Copying features, Marc Logghe
RE: Reliable working version of Biosql, Hilmar Lapp
RE: Reliable working version of Biosql, Hilmar Lapp
RE: directory for bioperl maintenance scripts, Hilmar Lapp
RE: Copying features, Hilmar Lapp
Re: Slow restriction digestion, Rob Edwards
Re: BIOPERL_SAVVY?, Jason Stajich
Re: Slow restriction digestion, Shawn Hoon
tests needed!, Heikki Lehvaslaiho
Slow restriction digestion, anthony . underwood
Re: directory for bioperl maintenance scripts, Heikki Lehvaslaiho
Re: Re: pfam/swissprot domain info, Jason Stajich
Re: Bio::Graphics problem, Lincoln Stein
Re: Bio::DB::Query::GenBank, Lincoln Stein
Re: Bio::DB::Query::GenBank, Lincoln Stein
Re: Can Bio::Graphics render a muti_segments picture?, Lincoln Stein
Re: BIOPERL_SAVVY?, Lincoln Stein
RE: BIOPERL_SAVVY?, Brian Osborne
Reliable working version of Biosql, Zayed Albertyn
Can Bio::Graphics render a muti_segments picture?, tongw
directory for bioperl maintenance scripts, Heikki Lehvaslaiho
Re: PrimarySeqI.pm patch [was Re: Copying features], Heikki Lehvaslaiho
Re: BIOPERL_SAVVY?, Heikki Lehvaslaiho
Re: problem with StandAloneBlast, James Wasmuth
Re: pfam/swissprot domain info, Douglas Kojetin
Re: problem with StandAloneBlast, Qiang Tu
Re: BIOPERL_SAVVY?, Lincoln Stein

May 11, 2003

problem with StandAloneBlast, ying lin
Re: split-like function, Rob Edwards
PrimarySeqI.pm patch [was Re: Copying features], Rob Edwards
RE: Copying features, Marc Logghe
pfam/swissprot domain info, Douglas Kojetin
Copying features, Rob Edwards
split-like function, Keith Boroevich

May 10, 2003

BIOPERL_SAVVY?, Ewan Birney
Pictogram, Shawn Hoon

May 09, 2003

Re: Graphics/Panel problem, Jason Stajich
Graphics/Panel problem, Thomas Keller
RE: bpindex.pl in sun solaris (sparc), Brian Osborne
bpindex.pl in sun solaris (sparc), Soumyadeep nandi

May 08, 2003

Re: CVS directory delete, James Stalker
Re: CVS directory delete, Juguang Xiao
Re: CVS directory delete, James Stalker
CVS directory delete, Juguang Xiao
Re: (repost) virtual gel from chromatogram, staden library on Windows, Remo Sanges
RE: STDOUT write_seq, Marc Logghe
STDOUT write_seq, Guido Dieterich

May 07, 2003

Re: bl2seq and disappearing variables, Jason Stajich
bl2seq and disappearing variables, James Wasmuth
bl2seq and disappearing variables, James Wasmuth
bioperl-l list back from the dead --- sorry for todays mail flood, Chris Dagdigian
Re: problem with Bio::SeqIO->write_seq, Jason Stajich
Re: Taxonomy and get_taxaid, Jason Stajich
Re: SeqIO/genbank makes false assumption?, Jason Stajich
Re: Bioperl-l Digest, Vol 1, Issue 1 (Eric E. Snyder: incommunicado), Eric Snyder
Re: SeqIO/genbank makes false assumption?, Ewan Birney
module announcement: Bio::OntologyIO::simplehierarchy, Allen Day
Re: module, Jason Stajich
(repost) virtual gel from chromatogram, staden library on Windows, Jonathan Epstein
Re: Taxonomy and get_taxaid, Jason Stajich
Re: Taxonomy and get_taxaid, Heikki Lehvaslaiho
Re: Taxonomy and get_taxaid, Heikki Lehvaslaiho
RE: problem with Bio::SeqIO->write_seq, Brian Osborne
Re: misleading error messages..., Jason Stajich
Re: Bioperl and ClustalW/Clustal, Jason Stajich
Bio::Graphics problem, Chris
About uninitiated string problem, darson
Taxonomy and get_taxaid, anthony . underwood
misleading error messages..., Alok Saldanha
SeqIO/genbank makes false assumption?, Mark Wilkinson
[offtopic] please delete me --- test to see if bioperl-l list is still dead, Chris Dagdigian
Bio::DB::Query::GenBank, Josh Lauricha
virtual gel from chromatogram, staden library on Windows, Jonathan Epstein
Volunteering, Chris Moy
[Fwd: Taxonomy and get_taxaid], chris dagdigian
Taxonomy and get_taxaid, anthony . underwood
Re: Error running BPbl2seq, BHurwitz
Scale with Bio::Grahics for upstream regions, Joao Magalhaes
Bioperl and ClustalW/Clustal, Hrishi
module, mlobo
Re: Miller-Myers Algorithm, Yee Man
problem with Bio::SeqIO->write_seq, Prachi Shah
Taxonomy and get_taxaid, anthony . underwood
locuslink.pm questions (for Keith Ching/Hilmar ?), Andrew Macgregor
An unsolved problem regarding RemoteBlast?, Joao Magalhaes
Bio::DB::GenBank->get_Stream_by_query, Josh Lauricha
Re: A pattern problem in Perl, Peter Wilkinson

May 01, 2003

Re: A pattern problem in Perl, Andrew Dalke
A pattern problem in Perl, darson

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