lang.perl.bio.general (thread)

bl2seq no hit error, Christopher Bouton
Bio::Matrix::PhylipDist, Jack Chen
- Re: Bio::Matrix::PhylipDist, Jason Stajich
Getting UTRs, Michael Muratet
- Re: Getting UTRs, Stephen Baird
BPbl2seq problem, Debashis Rana
HSPs: getting the location of mismatch, Charles Hauser
- Re: HSPs: getting the location of mismatch, Jason Stajich
- Re: HSPs: getting the location of mismatch, Peter Wilkinson
Bio::Index::Fasta return object problem, david vilanova
- RE: Bio::Index::Fasta return object problem, Brian Osborne
  - RE: Bio::Index::Fasta return object problem, david vilanova
    - RE: Bio::Index::Fasta return object problem, Brian Osborne
    - RE: Bio::Index::Fasta return object problem, david vilanova
    - Re: RE: Bio::Index::Fasta return object problem, Jason Stajich
- Re: Bio::Index::Fasta return object problem, Jason Stajich
  - Re: Bio::Index::Fasta return object problem, david vilanova
    - RE: Bio::Index::Fasta return object problem, Brian Osborne
    - Re: Re: Bio::Index::Fasta return object problem, Jason Stajich
Algorithm::Cluster for clustering gene expression data, Michiel Jan Laurens de Hoon
bl2seq parsing in SearchIO, Jason Stajich
Retrieving protein, Eric Wang
Bio::SearchIO broken in bioperl-live by missing Iteration/GenericIteration module, Matthew Vaughn
- Re: Bio::SearchIO broken in bioperl-live by missing Iteration/GenericIteration module, Jason Stajich
Genemark doesn't work with Prokaryotic model results, Thomas Keller
- Re: Genemark doesn't work with Prokaryotic model results, Heikki Lehvaslaiho
seqconvert, Heikki Lehvaslaiho
StandAloneBlast, Holzwarth,James,LAUSANNE,NRC/BS
- Re: StandAloneBlast, Prachi Shah
  - Re: StandAloneBlast, Jason Stajich
usage question, Genemark parser, Thomas Keller
- Re: usage question, Genemark parser, Jason Stajich
writing a parser, nkuipers
Geneid parser, Eric Just
- Re: Geneid parser, Keith James
Bio::Tools::Genemark question, Charles Hauser
- Re: Bio::Tools::Genemark question, Heikki Lehvaslaiho
changes in Analysis/soap.pm, Martin Senger
megablast parsing broken?, Neil Saunders
- Re: megablast parsing broken?, Jason Stajich
  - Re: megablast parsing broken?, Neil Saunders
    - Re: megablast parsing broken?, Jason Stajich
    - Re: megablast parsing broken?, Neil Saunders
RE: Implemented Miller-Myers alignment algorithm It turns out my program even outperforms Phil Green's implementation. It is 10% faster and uses only one-tenth of memory. You can download my code from http://www.stanford.edu/~yeeman/global.tgz. Here is the performance comparison: example I used: t1.fa and t2.fa at http://www.stanford.edu/~yeeman/ Both are DNA sequences with about 9800bp compiler for both ssearch34 and my program: gcc -g command line: ./ssearch34 -n -3 -q -H -f 3 -g 1 -d 1 -r "3/-1" -b 1 t1.fa t2.fa ./global t1.fa t2.fa ssearch34: 13.5 sec to find score 1 min 9 sec to calculate local alignment If it takes two score calculation to find the end points of lcoal alignment, the global alignment time will be 42 sec. Uses 15MB of RAM My Miller-Myers implementation: 38 sec to calculate alignment Uses 1.3MB of RAM, William R.Pearson
Biosql schema for use w/ bioperl-1.2.1, Steve Mathias
- Re: Biosql schema for use w/ bioperl-1.2.1, Hilmar Lapp
  - Re: Biosql schema for use w/ bioperl-1.2.1, Steve Mathias
  - Re: Biosql schema for use w/ bioperl-1.2.1, Steve Mathias
[ANNOUNCE] Modules for wrapping analysis CGIs, Heikki Lehvaslaiho
Using BioPerl for ACeDB Blixem?, cyril
PRANK CALLS, PRANK CALLS
Re: [apollo] Game XML parser, Lincoln Stein
How to get the corresponding DNA sequence of a protein gi#??, Sally Li
- Re: How to get the corresponding DNA sequence of a protein gi#??, Jason Stajich
  - Re: How to get the corresponding DNA sequence of a protein gi#??, Sally Li
  - Is this a bug? ?, Sally Li
Fatal Error: Arg list too long, Yasmina Sanchez
Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references, Hilmar Lapp
- Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references, Elia Stupka
  - Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references, Hilmar Lapp
    - Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references, Elia Stupka
    - Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references, Hilmar Lapp
    - Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references, Hilmar Lapp
Doesn't hurt to ask, Joao Magalhaes
- Re: Doesn't hurt to ask, Siddhartha Basu
- RE: Doesn't hurt to ask, Brian Osborne
Automated Medline searches, Joao Magalhaes
- Re: Automated Medline searches, Jason Stajich
Loading SwissProt Data into Oracle, Neil Evans
- Re: Loading SwissProt Data into Oracle, Jason Stajich
  - Re: Loading SwissProt Data into Oracle, Ewan Birney
    - Re: Loading SwissProt Data into Oracle, Hilmar Lapp
blat format parser for Bio::SearchIO?, Matthew Betts
- Re: blat format parser for Bio::SearchIO?, Jason Stajich
- Re: blat format parser for Bio::SearchIO?, Jason Stajich
BioSQL, Prachi Shah
- Re: BioSQL, Hilmar Lapp
date stamp in genbank file, Ben Snyder
- Re: date stamp in genbank file, Jason Stajich
Auto-response for your message to bioperl-bugs@xxxxxxxxxxx, bioperl-bugs-bounces
Your message to Bioperl-bugs awaits moderator approval, bioperl-bugs-bounces
Question about embl format, Lincoln Stein
- Re: Question about embl format, Ewan Birney
  - Re: Question about embl format, Lincoln Stein
    - Re: Question about embl format, Ewan Birney
    - Re: Question about embl format, Lincoln Stein
    - Re: Question about embl format, Ewan Birney
    - Re: Question about embl format, Hilmar Lapp
    - Re: Question about embl format, Lincoln Stein
- Re: Question about embl format, Heikki Lehvaslaiho
  - Re: Question about embl format, Lincoln Stein
[ANNOUNCE] tab sequence file format, Heikki Lehvaslaiho
how to get positive and frame in blastx use searchio?, Magic Fang
- Re: how to get positive and frame in blastx use searchio?, Jason Stajich
- RE: how to get positive and frame in blastx use searchio?, Brian Osborne
Mac OS X "build from source" instructions for perl 5.8.0 online at apple.com, chris dagdigian
- Re: Mac OS X "build from source" instructions for perl 5.8.0 online at apple.com, Lai Loong Fong
What is MPsrch?, Yee Man
- Re: What is MPsrch?, Heikki Lehvaslaiho
  - Re: What is MPsrch?, Yee Man
    - Re: What is MPsrch?, Aaron J Mackey
    - Implemented Miller-Myers alignment algorithm, Yee Man
    - Implemented Miller-Myers algorithm for local alignment, Yee Man
    - Briefings in Bioinformatics, Sergiy Ivakhno
- Re: What is MPsrch?, William R.Pearson
"Too many files open" with bl2seq, Peter Schattner
- Re: "Too many files open" with bl2seq, Steven Cannon
  - Re: "Too many files open" with bl2seq, Peter Schattner
    - Re: "Too many files open" with bl2seq, Steven Cannon
    - RE: Re: "Too many files open" with bl2seq, Jamie Hatfield \(AGCoL\)
    - RE: Re: "Too many files open" with bl2seq, Jason Stajich
Bio::Ontology::simpleGOparser, Christian Greggio
- Re: Bio::Ontology::simpleGOparser, Hilmar Lapp
(live-code) treeio warning, Jason Stajich
problems converting bsml to another file type, Clancy, Kevin
- Re: problems converting bsml to another file type, Charles Tilford
  - RE: problems converting bsml to another file type, Kevin Clancy
sim4 to GFF, Charles Hauser
- Re: sim4 to GFF, Hilmar Lapp
One more about swiss parsing, Elia Stupka
- Re: One more about swiss parsing, Hilmar Lapp
data class for swissprot, Elia Stupka
- Re: data class for swissprot, Hilmar Lapp
Re: [BioPython] NCBI: from protein to CDS, Jason Stajich
Isn't there Bio::Tools::Run for Phred, Chad Matsalla
- Re: Isn't there Bio::Tools::Run for Phred, Robson Francisco de Souza
  - Re: Isn't there Bio::Tools::Run for Phred, Chad Matsalla
Re: [Bioperl-guts-l] SeqIO does not work with raw mode?, Jason Stajich
Bio::Index::Fasta foreach loop, Ann Hedley
- Re: Bio::Index::Fasta foreach loop, Jason Stajich
- RE: Bio::Index::Fasta foreach loop, Brian Osborne
RE: more question about extracting information from G FF file, Marc Logghe
Isn't there Bio::Tools::Run for Phred?, Sang Chul Choi
Re the last message, Mikhail Esteves
Error running BPbl2seq, Mikhail Esteves
- RE: Error running BPbl2seq, Brian Osborne
more question about extracting information from GFF file, Jack Chen
Bio::SearchIO::blast, Josh Lauricha
- RE: Bio::SearchIO::blast, Brian Osborne
exception parsing plain old blast html, nkuipers
- Re: exception parsing plain old blast html, Jason Stajich
- RE: exception parsing plain old blast html, nkuipers
- RE: exception parsing plain old blast html, simon andrews (BI)
Bioperl-db install problems on macosx, Adam Witney
- Re: Bioperl-db install problems on macosx, Jason Stajich
  - Re: Bioperl-db install problems on macosx, Adam Witney
    - Re: Bioperl-db install problems on macosx, Hilmar Lapp
    - Re: Bioperl-db install problems on macosx, Adam Witney
    - Re: Bioperl-db install problems on macosx, Jason Stajich
    - Re: Bioperl-db install problems on macosx, Hilmar Lapp
  - Re: Bioperl-db install problems on macosx, Hilmar Lapp
Fwd: Perl program blowing up in IO.pm, Hilmar Lapp
- Fwd: Perl program blowing up in IO.pm, Hilmar Lapp
SearchIO update, Steve Chervitz
- SearchIO update, Steve Chervitz
Retrieve FASTA seqs with NCBI definition line, Mikaela Ilinca Gabrielli
- Re: Retrieve FASTA seqs with NCBI definition line, Heikki Lehvaslaiho
- RE: Retrieve FASTA seqs with NCBI definition line, Mikaela Ilinca Gabrielli
  - RE: Retrieve FASTA seqs with NCBI definition line, Jason Stajich
Project suggestion: Restriction Enzyme Analysis, Heikki Lehvaslaiho
- Re: Project suggestion: Restriction Enzyme Analysis, Steve Chervitz
  - Re: Project suggestion: Restriction Enzyme Analysis, Rob Edwards
    - Re: Project suggestion: Restriction Enzyme Analysis, Rob Edwards
    - Project suggestion: Restriction Enzyme Analysis, Peter Wilkinson
    - Re: Project suggestion: Restriction Enzyme Analysis, Heikki Lehvaslaiho
    - Message not available
    - Re: Project suggestion: Restriction Enzyme Analysis, Heikki Lehvaslaiho
- Re: Project suggestion: Restriction Enzyme Analysis, Neill White
  - Re: Project suggestion: Restriction Enzyme Analysis, Rob Edwards
    - Re: Project suggestion: Restriction Enzyme Analysis, Heikki Lehvaslaiho
[ANNOUNCE] Sequences with meta data, Heikki Lehvaslaiho
- [ANNOUNCE] Sequences with meta data, Richard Adams
  - Re: [ANNOUNCE] Sequences with meta data, Heikki Lehvaslaiho
    - Re: [ANNOUNCE] Sequences with meta data, Heikki Lehvaslaiho
[Fwd: Re: Re: Bio::Taxonomy::Tree], Heikki Lehvaslaiho
bioperl 1.2.1 install, Charles Hauser
- Re: bioperl 1.2.1 install, Hilmar Lapp
RE: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio: :SeqFeature::Primer, anthony . underwood
- Re: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer, Rob Edwards
  - Re: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer, Jayaprakash Rudraraju
    - Re: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer, Rob Edwards
- RE: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio: :SeqFeature::Primer, anthony . underwood
extracting 'comments' from gff-ver 2, Charles Hauser
- RE: extracting 'comments' from gff-ver 2, Cook, Malcolm
  - RE: extracting 'comments' from gff-ver 2, Charles Hauser
- RE: extracting 'comments' from gff-ver 2, Cook, Malcolm
Some comments on the Tool::Run::Pylo/Phylip module cluster, Babenko, Vladimir
Re: Fwd: [GMOD-devel] GO::TermFinder Announcement, Gavin Sherlock
- RE: Fwd: [GMOD-devel] GO::TermFinder Announcement, Brian Osborne
  - Re: Fwd: [GMOD-devel] GO::TermFinder Announcement, Gavin Sherlock
Extracting gi no from refseq record, Siddhartha Basu
- Re: Extracting gi no from refseq record, Jason Stajich
  - Re: Extracting gi no from refseq record, Siddhartha Basu
    - Re: Extracting gi no from refseq record, Jason Stajich
  - Re: Extracting gi no from refseq record, Hilmar Lapp
    - Re: Extracting gi no from refseq record, Siddhartha Basu
    - Re: Extracting gi no from refseq record, Hilmar Lapp
    - Re: Extracting gi no from refseq record, Hilmar Lapp
    - Re: Extracting gi no from refseq record, Siddhartha Basu
    - Re: Extracting gi no from refseq record, Hilmar Lapp
    - Re: Extracting gi no from refseq record, Siddhartha Basu
    - Re: Extracting gi no from refseq record, Hilmar Lapp
    - Re: Extracting gi no from refseq record, Siddhartha Basu
    - Re: Extracting gi no from refseq record, Jason Stajich
    - Re: Extracting gi no from refseq record, Hilmar Lapp
    - Re: Extracting gi no from refseq record, Siddhartha Basu
- Re: Extracting gi no from refseq record, Hilmar Lapp
Re: gbrowse support for file-based databases, Scott Cain
- Re: Re: gbrowse support for file-based databases, Lincoln Stein
Bio::Taxonomy::Tree, Qiang Tu
- Re: Bio::Taxonomy::Tree, Heikki Lehvaslaiho
  - Re: Bio::Taxonomy::Tree, Heikki Lehvaslaiho
- Re: Bio::Taxonomy::Tree, Rob Edwards
- Re: Re: Bio::Taxonomy::Tree, Qiang TU
- Re: Re: Bio::Taxonomy::Tree, Qiang TU
  - Re: Re: Bio::Taxonomy::Tree, Heikki Lehvaslaiho
- Fw: Re: Re: Bio::Taxonomy::Tree, Qiang Tu
Re: [Bioperl-guts-l] Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm line 614, Jason Stajich
Re: common ancestor for ontology terms, Hilmar Lapp
- Re: common ancestor for ontology terms, Hilmar Lapp
suggestion for a new module, Mikaela Ilinca Gabrielli
- Re: suggestion for a new module, Heikki Lehvaslaiho
directory for config files, Heikki Lehvaslaiho
- Re: directory for config files, Hilmar Lapp
- Re: directory for config files, Lincoln Stein
- RE: directory for config files, Cook, Malcolm
New analysis interface; name space question, Heikki Lehvaslaiho
- New analysis interface; name space question, Richard Adams
  - Re: New analysis interface; name space question, Heikki Lehvaslaiho
FeatureFile and pad_left, Ken
Bioperl and BioSQL status, William Hsiao
- Re: Bioperl and BioSQL status, Chris Mungall
- Re: [BioSQL-l] Bioperl and BioSQL status, Hilmar Lapp
Problem with accession number in Genbank, William Boileau
cvs modules?, Heikki Lehvaslaiho
- Re: cvs modules?, Jason Stajich
  - Re: cvs modules?, Heikki Lehvaslaiho
    - Re: cvs modules?, Hilmar Lapp
- Re: cvs modules?, Hilmar Lapp
Re: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer, Rob Edwards
- Re: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer, Ewan Birney
  - Re: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer, Rob Edwards
- Re: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer, Jason Stajich
  - Re: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer, Rob Edwards
  - Re: Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer, Hilmar Lapp
Re: {SPECS] Sequence meta data, Peter Schattner
- Re: {SPECS] Sequence meta data, Heikki Lehvaslaiho
  - Re: {SPECS] Sequence meta data, Peter Schattner
  - Re: {SPECS] Sequence meta data, Lincoln Stein
Fwd: APRIL FOOLS DAY PRANK, Cynthia