April 2003 Archives by thread

• Messages sorted by: [ subject ] [ author ] [ date ]
• More info on this list...

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   Hilmar Lapp
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Ewan Birney
  • [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer   Rob Edwards
• [Bioperl-l] {SPECS] Sequence meta data   Heikki Lehvaslaiho
  • [Bioperl-l] {SPECS] Sequence meta data   Peter Schattner
  • [Bioperl-l] {SPECS] Sequence meta data   Lincoln Stein
• [Bioperl-l] cvs modules?   Heikki Lehvaslaiho
  • [Bioperl-l] cvs modules?   Jason Stajich
    • [Bioperl-l] cvs modules?   Heikki Lehvaslaiho
      • [Bioperl-l] cvs modules?   Hilmar Lapp
  • [Bioperl-l] cvs modules?   Hilmar Lapp
• [Bioperl-l] FeatureFile and pad_left   Ken
• [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   Heikki Lehvaslaiho
  • [Bioperl-l] directory for config files   Hilmar Lapp
  • [Bioperl-l] directory for config files   Lincoln Stein
• [Bioperl-l] directory for config files   Cook, Malcolm
• [Bioperl-l] suggestion for a new module   Mikaela Ilinca Gabrielli
  • [Bioperl-l] suggestion for a new module   Heikki Lehvaslaiho
• [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   Brian Osborne
    • [Bioperl-l] Fwd: [GMOD-devel] GO::TermFinder Announcement   Gavin Sherlock
• [Bioperl-l] Re: gbrowse support for file-based databases   Scott Cain
  • [Bioperl-l] Re: gbrowse support for file-based databases   Lincoln Stein
• [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   Jason Stajich
    • [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   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   Hilmar Lapp
      • [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   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   Hilmar Lapp
• [Bioperl-l] New analysis interface; name space question   Richard Adams
  • [Bioperl-l] New analysis interface; name space question   Heikki Lehvaslaiho
• [Bioperl-l] Some comments on the Tool::Run::Pylo/Phylip module cluster   Babenko, Vladimir
• [Bioperl-l] Bio::Taxonomy::Tree   Qiang Tu
  • [Bioperl-l] Bio::Taxonomy::Tree   Rob Edwards
  • [Bioperl-l] Bio::Taxonomy::Tree   Heikki Lehvaslaiho
    • [Bioperl-l] Bio::Taxonomy::Tree   Heikki Lehvaslaiho
• [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] bioperl 1.2.1 install   Charles Hauser
  • [Bioperl-l] bioperl 1.2.1 install   Hilmar Lapp
• [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   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   Rob Edwards
• [Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio: :SeqFeature::Primer   anthony.underwood at hpa.org.uk
• [Bioperl-l] Bio::Taxonomy::Tree   Qiang TU
• [Bioperl-l] Bio::Taxonomy::Tree   Qiang TU
  • [Bioperl-l] Bio::Taxonomy::Tree   Heikki Lehvaslaiho
• [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] 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   Rob Edwards
      • [Bioperl-l] Project suggestion: Restriction Enzyme Analysis   Peter Wilkinson
      • [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] Retrieve FASTA seqs with NCBI definition line   Jason Stajich
• [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] exception parsing plain old blast html   nkuipers
  • [Bioperl-l] exception parsing plain old blast html   Jason Stajich
• [Bioperl-l] Bio::SearchIO::blast   Josh Lauricha
  • [Bioperl-l] Bio::SearchIO::blast   Brian Osborne
• [Bioperl-l] exception parsing plain old blast html   nkuipers
• [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] Bioperl-db install problems on macosx   Adam Witney
  • [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   Adam Witney
      • [Bioperl-l] Bioperl-db install problems on macosx   Hilmar Lapp
      • [Bioperl-l] Bioperl-db install problems on macosx   Adam Witney
      • [Bioperl-l] Bioperl-db install problems on macosx   Hilmar Lapp
      • [Bioperl-l] Bioperl-db install problems on macosx   Jason Stajich
• [Bioperl-l] more question about extracting information from GFF file   Jack Chen
• [Bioperl-l] Error running BPbl2seq   Mikhail Esteves
  • [Bioperl-l] Error running BPbl2seq   Brian Osborne
• [Bioperl-l] Re the last message   Mikhail Esteves
• [Bioperl-l] Re: [Bioperl-guts-l] SeqIO does not work with raw mode?   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] Bio::Index::Fasta foreach loop   Brian Osborne
  • [Bioperl-l] Bio::Index::Fasta foreach loop   Jason Stajich
• [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] Re: [BioPython] NCBI: from protein to CDS   Jason Stajich
• [Bioperl-l] data class for swissprot   Elia Stupka
  • [Bioperl-l] data class for swissprot   Hilmar Lapp
• [Bioperl-l] One more about swiss parsing   Elia Stupka
  • [Bioperl-l] One more about swiss parsing   Hilmar Lapp
• [Bioperl-l] sim4 to GFF   Charles Hauser
  • [Bioperl-l] sim4 to GFF   Hilmar Lapp
• [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] RE: problems converting bsml to another file type   Kevin Clancy
• [Bioperl-l] (live-code) treeio warning   Jason Stajich
• [Bioperl-l] Bio::Ontology::simpleGOparser   Christian Greggio
  • [Bioperl-l] Bio::Ontology::simpleGOparser   Hilmar Lapp
• [Bioperl-l] "Too many files open" with bl2seq   Peter Schattner
• [Bioperl-l] What is MPsrch?   Yee Man
  • [Bioperl-l] What is MPsrch?   Heikki Lehvaslaiho
    • [Bioperl-l] What is MPsrch?   Yee Man
      • [Bioperl-l] What is MPsrch?   Aaron J Mackey
      • [Bioperl-l] Implemented Miller-Myers alignment algorithm   Yee Man
      • [Bioperl-l] Implemented Miller-Myers algorithm for local alignment   Yee Man
      • [Bioperl-l] Briefings in Bioinformatics   Sergiy Ivakhno
• [Bioperl-l] Mac OS X "build from source" instructions for perl 5.8.0 online at apple.com   chris dagdigian
  • [Bioperl-l] Mac OS X "build from source" instructions for perl 5.8.0 online at apple.com   Lai Loong Fong
• [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] What is MPsrch?   William R.Pearson
• [Bioperl-l] Re: "Too many files open" with bl2seq   Steven Cannon
  • [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   Jamie Hatfield (AGCoL)
      • [Bioperl-l] Re: "Too many files open" with bl2seq   Jason Stajich
• [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   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] Question about embl format   Heikki Lehvaslaiho
    • [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] 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] how to get positive and frame in blastx use searchio?   Magic Fang
  • [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] blat format parser for Bio::SearchIO?   Matthew Betts
  • [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   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] Automated Medline searches   Joao Magalhaes
  • [Bioperl-l] Automated Medline searches   Jason Stajich
• [Bioperl-l] Doesn't hurt to ask   Joao Magalhaes
  • [Bioperl-l] Doesn't hurt to ask   Siddhartha Basu
  • [Bioperl-l] Doesn't hurt to ask   Brian Osborne
• [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   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   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] How to get the corresponding DNA sequence of a protein gi#??   Jason Stajich
    • [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] Re: [apollo] Game XML parser   Lincoln Stein
• [Bioperl-l] PRANK CALLS   PRANK CALLS
• [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] [ANNOUNCE] Modules for wrapping analysis CGIs   Heikki Lehvaslaiho
• [Bioperl-l] Using BioPerl for ACeDB Blixem?   cyril at pacific.net.sg
• [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] Project suggestion: Restriction Enzyme Analysis   Heikki Lehvaslaiho
• [Bioperl-l] changes in Analysis/soap.pm   Martin Senger
• [Bioperl-l] Bio::Tools::Genemark question   Charles Hauser
  • [Bioperl-l] Bio::Tools::Genemark question   Heikki Lehvaslaiho
• [Bioperl-l] megablast parsing broken?   Neil Saunders
  • [Bioperl-l] megablast parsing broken?   Jason Stajich
    • [Bioperl-l] megablast parsing broken?   Neil Saunders
      • [Bioperl-l] megablast parsing broken?   Jason Stajich
      • [Bioperl-l] megablast parsing broken?   Neil Saunders
• [Bioperl-l] Geneid parser   Eric Just
  • [Bioperl-l] Geneid parser   Keith James
• [Bioperl-l] writing a parser   nkuipers
• [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] StandAloneBlast   Prachi Shah
    • [Bioperl-l] StandAloneBlast   Jason Stajich
• [Bioperl-l] Genemark doesn't work with Prokaryotic model results   Thomas Keller
  • [Bioperl-l] Genemark doesn't work with Prokaryotic model results   Heikki Lehvaslaiho
• [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] bl2seq parsing in SearchIO   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
  • [Bioperl-l] Bio::Index::Fasta return object problem   Brian Osborne
    • RE: [Bioperl-l] Bio::Index::Fasta return object problem   david vilanova
      • [Bioperl-l] Bio::Index::Fasta return object problem   Brian Osborne
      • RE: [Bioperl-l] Bio::Index::Fasta return object problem   david vilanova
      • RE: [Bioperl-l] Bio::Index::Fasta return object problem   Jason Stajich
  • [Bioperl-l] Bio::Index::Fasta return object problem   Jason Stajich
    • Re: [Bioperl-l] Bio::Index::Fasta return object problem   david vilanova
      • [Bioperl-l] Bio::Index::Fasta return object problem   Brian Osborne
      • Re: [Bioperl-l] Bio::Index::Fasta return object problem   Jason Stajich
• [Bioperl-l] Getting UTRs   Michael Muratet
  • [Bioperl-l] Getting UTRs   Stephen Baird
• [Bioperl-l] BPbl2seq problem   Debashis Rana
• [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

• Messages sorted by: [ subject ] [ author ] [ date ]
• More info on this list...