April 2003 Archives by author

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

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

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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• More info on this list...