April 2003 Archives by subject

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Starting: Tue Apr 1 02:38:03 EDT 2003
Ending: Wed Apr 30 23:49:32 EDT 2003
Messages: 247

• RE: [Bioperl-l] Bio::Index::Fasta return object problem   Jason Stajich
• Re: [Bioperl-l] Bio::Index::Fasta return object problem   Jason Stajich
• RE: [Bioperl-l] Bio::Index::Fasta return object problem   david vilanova
• RE: [Bioperl-l] Bio::Index::Fasta return object problem   david vilanova
• Re: [Bioperl-l] Bio::Index::Fasta return object problem   david vilanova
• [Bioperl-l] Auto-response for your message to bioperl-bugs@bioperl.org   bioperl-bugs-bounces at bioperl.org
• [Bioperl-l] How to get the corresponding DNA sequence of a protein gi#??   Sally Li
• [Bioperl-l] more question about extracting information from GFF file   Jack Chen
• [Bioperl-l] Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references   Hilmar Lapp
• [Bioperl-l] Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references   Hilmar Lapp
• [Bioperl-l] Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references   Hilmar Lapp
• [Bioperl-l] Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references   Hilmar Lapp
• [Bioperl-l] Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references   Elia Stupka
• [Bioperl-l] Re: [BioSQL-l] Bug in loading duplicate but non-identical swissprot references   Elia Stupka
• [Bioperl-l] Some comments on the Tool::Run::Pylo/Phylip module cluster   Babenko, Vladimir
• [Bioperl-l] Mac OS X "build from source" instructions for perl 5.8.0 online at apple.com   chris dagdigian
• [Bioperl-l] 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
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Rob Edwards
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Rob Edwards
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Hilmar Lapp
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Jason Stajich
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Ewan Birney
• [Bioperl-l] How to get the corresponding DNA sequence of a protein gi#??   Sally Li
• [Bioperl-l] How to get the corresponding DNA sequence of a protein gi#??   Jason Stajich
• [Bioperl-l] Mac OS X "build from source" instructions for perl 5.8.0 online at apple.com   Lai Loong Fong
• [Bioperl-l] "Too many files open" with bl2seq   Peter Schattner
• [Bioperl-l] (live-code) treeio warning   Jason Stajich
• [Bioperl-l] [ANNOUNCE] Modules for wrapping analysis CGIs   Heikki Lehvaslaiho
• [Bioperl-l] [ANNOUNCE] Sequences with meta data   Heikki Lehvaslaiho
• [Bioperl-l] [ANNOUNCE] Sequences with meta data   Richard Adams
• [Bioperl-l] [ANNOUNCE] Sequences with meta data   Heikki Lehvaslaiho
• [Bioperl-l] [ANNOUNCE] Sequences with meta data   Heikki Lehvaslaiho
• [Bioperl-l] [ANNOUNCE] tab sequence file format   Heikki Lehvaslaiho
• [Bioperl-l] A pattern problem in Perl   Andrew Dalke
• [Bioperl-l] Algorithm::Cluster for clustering gene expression data   Michiel Jan Laurens de Hoon
• [Bioperl-l] Automated Medline searches   Jason Stajich
• [Bioperl-l] Automated Medline searches   Joao Magalhaes
• [Bioperl-l] Bio::Index::Fasta foreach loop   Brian Osborne
• [Bioperl-l] Bio::Index::Fasta foreach loop   Jason Stajich
• [Bioperl-l] Bio::Index::Fasta foreach loop   Ann Hedley
• [Bioperl-l] Bio::Index::Fasta return object problem   Brian Osborne
• [Bioperl-l] Bio::Index::Fasta return object problem   Brian Osborne
• [Bioperl-l] Bio::Index::Fasta return object problem   Jason Stajich
• [Bioperl-l] Bio::Index::Fasta return object problem   Brian Osborne
• [Bioperl-l] Bio::Index::Fasta return object problem   david vilanova
• [Bioperl-l] Bio::Matrix::PhylipDist   Jack Chen
• [Bioperl-l] Bio::Matrix::PhylipDist   Jason Stajich
• [Bioperl-l] Bio::Ontology::simpleGOparser   Christian Greggio
• [Bioperl-l] Bio::Ontology::simpleGOparser   Hilmar Lapp
• [Bioperl-l] Bio::SearchIO broken in bioperl-live by missing Iteration/GenericIteration module   Matthew Vaughn
• [Bioperl-l] Bio::SearchIO broken in bioperl-live by missing Iteration/GenericIteration module   Jason Stajich
• [Bioperl-l] Bio::SearchIO::blast   Josh Lauricha
• [Bioperl-l] Bio::SearchIO::blast   Brian Osborne
• [Bioperl-l] Bio::Taxonomy::Tree   Rob Edwards
• [Bioperl-l] Bio::Taxonomy::Tree   Heikki Lehvaslaiho
• [Bioperl-l] Bio::Taxonomy::Tree   Heikki Lehvaslaiho
• [Bioperl-l] Bio::Taxonomy::Tree   Heikki Lehvaslaiho
• [Bioperl-l] Bio::Taxonomy::Tree   Qiang TU
• [Bioperl-l] Bio::Taxonomy::Tree   Qiang TU
• [Bioperl-l] Bio::Taxonomy::Tree   Qiang Tu
• [Bioperl-l] Bio::Tools::Genemark question   Charles Hauser
• [Bioperl-l] Bio::Tools::Genemark question   Heikki Lehvaslaiho
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Rob Edwards
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Rob Edwards
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Jayaprakash Rudraraju
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio: :SeqFeature::Primer   anthony.underwood at hpa.org.uk
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio: :SeqFeature::Primer   anthony.underwood at hpa.org.uk
• [Bioperl-l] bioperl 1.2.1 install   Hilmar Lapp
• [Bioperl-l] bioperl 1.2.1 install   Charles Hauser
• [Bioperl-l] Bioperl and BioSQL status   William Hsiao
• [Bioperl-l] Bioperl and BioSQL status   Chris Mungall
• [Bioperl-l] Bioperl-db install problems on macosx   Hilmar Lapp
• [Bioperl-l] Bioperl-db install problems on macosx   Hilmar Lapp
• [Bioperl-l] Bioperl-db install problems on macosx   Jason Stajich
• [Bioperl-l] Bioperl-db install problems on macosx   Hilmar Lapp
• [Bioperl-l] Bioperl-db install problems on macosx   Jason Stajich
• [Bioperl-l] Bioperl-db install problems on macosx   Adam Witney
• [Bioperl-l] Bioperl-db install problems on macosx   Adam Witney
• [Bioperl-l] Bioperl-db install problems on macosx   Adam Witney
• [Bioperl-l] BioSQL   Prachi Shah
• [Bioperl-l] BioSQL   Hilmar Lapp
• [Bioperl-l] Biosql schema for use w/ bioperl-1.2.1   Steve Mathias
• [Bioperl-l] Biosql schema for use w/ bioperl-1.2.1   Hilmar Lapp
• [Bioperl-l] Biosql schema for use w/ bioperl-1.2.1   Steve Mathias
• [Bioperl-l] Biosql schema for use w/ bioperl-1.2.1   Steve Mathias
• [Bioperl-l] bl2seq parsing in SearchIO   Jason Stajich
• [Bioperl-l] blat format parser for Bio::SearchIO?   Jason Stajich
• [Bioperl-l] blat format parser for Bio::SearchIO?   Jason Stajich
• [Bioperl-l] blat format parser for Bio::SearchIO?   Matthew Betts
• [Bioperl-l] BPbl2seq problem   Debashis Rana
• [Bioperl-l] Briefings in Bioinformatics   Sergiy Ivakhno
• [Bioperl-l] changes in Analysis/soap.pm   Martin Senger
• [Bioperl-l] common ancestor for ontology terms   Hilmar Lapp
• [Bioperl-l] common ancestor for ontology terms   Hilmar Lapp
• [Bioperl-l] cvs modules?   Jason Stajich
• [Bioperl-l] cvs modules?   Hilmar Lapp
• [Bioperl-l] cvs modules?   Hilmar Lapp
• [Bioperl-l] cvs modules?   Heikki Lehvaslaiho
• [Bioperl-l] cvs modules?   Heikki Lehvaslaiho
• [Bioperl-l] data class for swissprot   Hilmar Lapp
• [Bioperl-l] data class for swissprot   Elia Stupka
• [Bioperl-l] date stamp in genbank file   Ben Snyder
• [Bioperl-l] date stamp in genbank file   Jason Stajich
• [Bioperl-l] directory for config files   Hilmar Lapp
• [Bioperl-l] directory for config files   Heikki Lehvaslaiho
• [Bioperl-l] directory for config files   Cook, Malcolm
• [Bioperl-l] directory for config files   Lincoln Stein
• [Bioperl-l] Doesn't hurt to ask   Siddhartha Basu
• [Bioperl-l] Doesn't hurt to ask   Joao Magalhaes
• [Bioperl-l] Doesn't hurt to ask   Brian Osborne
• [Bioperl-l] Error running BPbl2seq   Mikhail Esteves
• [Bioperl-l] Error running BPbl2seq   Brian Osborne
• [Bioperl-l] exception parsing plain old blast html   nkuipers
• [Bioperl-l] exception parsing plain old blast html   nkuipers
• [Bioperl-l] exception parsing plain old blast html   Jason Stajich
• [Bioperl-l] exception parsing plain old blast html   simon andrews (BI)
• [Bioperl-l] extracting 'comments' from gff-ver 2   Cook, Malcolm
• [Bioperl-l] extracting 'comments' from gff-ver 2   Charles Hauser
• [Bioperl-l] extracting 'comments' from gff-ver 2   Charles Hauser
• [Bioperl-l] extracting 'comments' from gff-ver 2   Cook, Malcolm
• [Bioperl-l] Extracting gi no from refseq record   Siddhartha Basu
• [Bioperl-l] Extracting gi no from refseq record   Jason Stajich
• [Bioperl-l] Extracting gi no from refseq record   Siddhartha Basu
• [Bioperl-l] Extracting gi no from refseq record   Hilmar Lapp
• [Bioperl-l] Extracting gi no from refseq record   Hilmar Lapp
• [Bioperl-l] Extracting gi no from refseq record   Hilmar Lapp
• [Bioperl-l] Extracting gi no from refseq record   Jason Stajich
• [Bioperl-l] Extracting gi no from refseq record   Siddhartha Basu
• [Bioperl-l] Extracting gi no from refseq record   Hilmar Lapp
• [Bioperl-l] Extracting gi no from refseq record   Hilmar Lapp
• [Bioperl-l] Extracting gi no from refseq record   Hilmar Lapp
• [Bioperl-l] Extracting gi no from refseq record   Siddhartha Basu
• [Bioperl-l] Extracting gi no from refseq record   Siddhartha Basu
• [Bioperl-l] Extracting gi no from refseq record   Hilmar Lapp
• [Bioperl-l] Extracting gi no from refseq record   Siddhartha Basu
• [Bioperl-l] Extracting gi no from refseq record   Jason Stajich
• [Bioperl-l] Extracting gi no from refseq record   Siddhartha Basu
• [Bioperl-l] Fatal Error: Arg list too long   Yasmina Sanchez
• [Bioperl-l] FeatureFile and pad_left   Ken
• [Bioperl-l] Fwd: [GMOD-devel] GO::TermFinder Announcement   Gavin Sherlock
• [Bioperl-l] Fwd: [GMOD-devel] GO::TermFinder Announcement   Gavin Sherlock
• [Bioperl-l] Fwd: [GMOD-devel] GO::TermFinder Announcement   Brian Osborne
• [Bioperl-l] Fwd: APRIL FOOLS DAY PRANK   Cynthia
• [Bioperl-l] Fwd: Perl program blowing up in IO.pm   Hilmar Lapp
• [Bioperl-l] Fwd: Perl program blowing up in IO.pm   Hilmar Lapp
• [Bioperl-l] Geneid parser   Eric Just
• [Bioperl-l] Geneid parser   Keith James
• [Bioperl-l] Genemark doesn't work with Prokaryotic model results   Heikki Lehvaslaiho
• [Bioperl-l] Genemark doesn't work with Prokaryotic model results   Thomas Keller
• [Bioperl-l] Getting UTRs   Michael Muratet
• [Bioperl-l] Getting UTRs   Stephen Baird
• [Bioperl-l] how to get positive and frame in blastx use searchio?   Jason Stajich
• [Bioperl-l] how to get positive and frame in blastx use searchio?   Brian Osborne
• [Bioperl-l] how to get positive and frame in blastx use searchio?   Magic Fang
• [Bioperl-l] HSPs: getting the location of mismatch   Charles Hauser
• [Bioperl-l] HSPs: getting the location of mismatch   Jason Stajich
• [Bioperl-l] HSPs: getting the location of mismatch   Peter Wilkinson
• [Bioperl-l] Implemented Miller-Myers algorithm for local alignment   Yee Man
• [Bioperl-l] Implemented Miller-Myers alignment algorithm   Yee Man
• [Bioperl-l] 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
• [Bioperl-l] Is this a bug? ?   Sally Li
• [Bioperl-l] Isn't there Bio::Tools::Run for Phred   Chad Matsalla
• [Bioperl-l] Isn't there Bio::Tools::Run for Phred   Robson Francisco de Souza
• [Bioperl-l] Isn't there Bio::Tools::Run for Phred   Chad Matsalla
• [Bioperl-l] Isn't there Bio::Tools::Run for Phred?   Sang Chul Choi
• [Bioperl-l] Loading SwissProt Data into Oracle   Neil Evans
• [Bioperl-l] Loading SwissProt Data into Oracle   Jason Stajich
• [Bioperl-l] Loading SwissProt Data into Oracle   Ewan Birney
• [Bioperl-l] Loading SwissProt Data into Oracle   Hilmar Lapp
• [Bioperl-l] megablast parsing broken?   Jason Stajich
• [Bioperl-l] megablast parsing broken?   Neil Saunders
• [Bioperl-l] megablast parsing broken?   Neil Saunders
• [Bioperl-l] megablast parsing broken?   Jason Stajich
• [Bioperl-l] megablast parsing broken?   Neil Saunders
• [Bioperl-l] more question about extracting information from G FF file   Marc Logghe
• [Bioperl-l] New analysis interface; name space question   Heikki Lehvaslaiho
• [Bioperl-l] New analysis interface; name space question   Richard Adams
• [Bioperl-l] New analysis interface; name space question   Heikki Lehvaslaiho
• [Bioperl-l] One more about swiss parsing   Hilmar Lapp
• [Bioperl-l] One more about swiss parsing   Elia Stupka
• [Bioperl-l] PRANK CALLS   PRANK CALLS
• [Bioperl-l] Problem with accession number in Genbank   William Boileau
• [Bioperl-l] problems converting bsml to another file type   Clancy, Kevin
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Heikki Lehvaslaiho
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Steve Chervitz
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Rob Edwards
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Neill White
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Rob Edwards
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Heikki Lehvaslaiho
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Rob Edwards
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Peter Wilkinson
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Heikki Lehvaslaiho
• [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Heikki Lehvaslaiho
• [Bioperl-l] Question about embl format   Lincoln Stein
• [Bioperl-l] Question about embl format   Ewan Birney
• [Bioperl-l] Question about embl format   Heikki Lehvaslaiho
• [Bioperl-l] Question about embl format   Lincoln Stein
• [Bioperl-l] Question about embl format   Lincoln Stein
• [Bioperl-l] Question about embl format   Ewan Birney
• [Bioperl-l] Question about embl format   Lincoln Stein
• [Bioperl-l] Question about embl format   Ewan Birney
• [Bioperl-l] Question about embl format   Hilmar Lapp
• [Bioperl-l] Question about embl format   Lincoln Stein
• [Bioperl-l] Re the last message   Mikhail Esteves
• [Bioperl-l] Re: "Too many files open" with bl2seq   Peter Schattner
• [Bioperl-l] Re: "Too many files open" with bl2seq   Steven Cannon
• [Bioperl-l] Re: "Too many files open" with bl2seq   Steven Cannon
• [Bioperl-l] Re: "Too many files open" with bl2seq   Jamie Hatfield (AGCoL)
• [Bioperl-l] Re: "Too many files open" with bl2seq   Jason Stajich
• [Bioperl-l] Re: [apollo] Game XML parser   Lincoln Stein
• [Bioperl-l] Re: [Bioperl-guts-l] SeqIO does not work with raw mode?   Jason Stajich
• [Bioperl-l] Re: [BioPython] NCBI: from protein to CDS   Jason Stajich
• [Bioperl-l] Re: [BioSQL-l] Bioperl and BioSQL status   Hilmar Lapp
• [Bioperl-l] Re: gbrowse support for file-based databases   Scott Cain
• [Bioperl-l] Re: gbrowse support for file-based databases   Lincoln Stein
• [Bioperl-l] Re: problems converting bsml to another file type   Charles Tilford
• [Bioperl-l] RE: problems converting bsml to another file type   Kevin Clancy
• [Bioperl-l] Retrieve FASTA seqs with NCBI definition line   Jason Stajich
• [Bioperl-l] Retrieve FASTA seqs with NCBI definition line   Mikaela Ilinca Gabrielli
• [Bioperl-l] Retrieve FASTA seqs with NCBI definition line   Heikki Lehvaslaiho
• [Bioperl-l] Retrieve FASTA seqs with NCBI definition line   Mikaela Ilinca Gabrielli
• [Bioperl-l] Retrieving protein   Eric Wang
• [Bioperl-l] SearchIO update   Steve Chervitz
• [Bioperl-l] SearchIO update   Steve Chervitz
• [Bioperl-l] seqconvert   Heikki Lehvaslaiho
• [Bioperl-l] sim4 to GFF   Charles Hauser
• [Bioperl-l] sim4 to GFF   Hilmar Lapp
• [Bioperl-l] StandAloneBlast   Holzwarth,James,LAUSANNE,NRC/BS
• [Bioperl-l] StandAloneBlast   Prachi Shah
• [Bioperl-l] StandAloneBlast   Jason Stajich
• [Bioperl-l] suggestion for a new module   Mikaela Ilinca Gabrielli
• [Bioperl-l] suggestion for a new module   Heikki Lehvaslaiho
• [Bioperl-l] usage question, Genemark parser   Thomas Keller
• [Bioperl-l] usage question, Genemark parser   Jason Stajich
• [Bioperl-l] Using BioPerl for ACeDB Blixem?   cyril at pacific.net.sg
• [Bioperl-l] What is MPsrch?   Yee Man
• [Bioperl-l] What is MPsrch?   Yee Man
• [Bioperl-l] What is MPsrch?   Heikki Lehvaslaiho
• [Bioperl-l] What is MPsrch?   Aaron J Mackey
• [Bioperl-l] What is MPsrch?   William R.Pearson
• [Bioperl-l] writing a parser   nkuipers
• [Bioperl-l] Your message to Bioperl-bugs awaits moderator approval   bioperl-bugs-bounces at bioperl.org
• [Bioperl-l] {SPECS] Sequence meta data   Heikki Lehvaslaiho
• [Bioperl-l] {SPECS] Sequence meta data   Peter Schattner
• [Bioperl-l] {SPECS] Sequence meta data   Lincoln Stein
• [Fwd: Re: Re: [Bioperl-l] Bio::Taxonomy::Tree]   Heikki Lehvaslaiho
• Fw: Re: Re: [Bioperl-l] Bio::Taxonomy::Tree   Qiang Tu

Last message date: Wed Apr 30 23:49:32 EDT 2003
Archived on: Thu May 1 00:48:42 EDT 2003

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