April 2003 Archives by date

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

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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