January 2003 Archives by author

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Starting: Wed Jan 1 02:59:01 EDT 2003
Ending: Fri Jan 31 21:47:12 EDT 2003
Messages: 275

• [Bioperl-l] Reverse Comp Coding Puzzler   Jamie Hatfield (AGCoL)
• [Bioperl-l] Biocorba   Nils Höglund
• [Bioperl-l] problems getting 1.2 tarball   Fernan Aguero
• [Bioperl-l] bioperl-1.2 : man pages?   Fernan Aguero
• [Bioperl-l] bioperl-1.2 : man pages?   Fernan Aguero
• [Bioperl-l] bioperl-1.2 : man pages?   Fernan Aguero
• [Bioperl-l] Determining strand orientation from bl2seq report   Dave Arenillas
• [Bioperl-l] Determining strand orientation from bl2seq report   Dave Arenillas
• [Bioperl-l] Determining strand orientation from bl2seq report   Dave Arenillas
• [Bioperl-l] problem with cvs server   Benjamin Berman
• [Bioperl-l] problem with cvs server   Benjamin Berman
• [Bioperl-l] negative reading frames in Search/HSP/BlastHSP.pm   Benjamin Berman
• [Bioperl-l] problems getting 1.2 tarball   Ewan Birney
• [Bioperl-l] bioperl-1.2 : man pages?   Ewan Birney
• [Bioperl-l] bioperl-1.2 : man pages?   Ewan Birney
• [Bioperl-l] problems getting 1.2 tarball   Ewan Birney
• [Bioperl-l] webstuff   Ewan Birney
• [Bioperl-l] Re: DNA Smith-Waterman code   Ewan Birney
• [Bioperl-l] Genbank/EMBL output   Ewan Birney
• [Bioperl-l] Installation of Bioperl   Ewan Birney
• [Bioperl-l] Genbank/EMBL output   Ewan Birney
• [Bioperl-l] Determining strand orientation from bl2seq report   Ewan Birney
• [Bioperl-l] circular refs/ unattach_seq in SeqFeatureI   Ewan Birney
• [Bioperl-l] Bioperl error : can't locate Bio/Tool/Run/WrapperBase.pm   Ewan Birney
• [Bioperl-l] circular refs/ unattach_seq in SeqFeatureI   Ewan Birney
• [Bioperl-l] biolinux.org: bioperl rpm   Ewan Birney
• [Bioperl-l] Permission denied when using Bio::SearchIO in CGI script   Ewan Birney
• [Bioperl-l] An update for my DNA Smith-Waterman code   Ewan Birney
• [Bioperl-l] Production scripts   Ewan Birney
• [Bioperl-l] problem with Bio::DB::Query::GenBank   Ewan Birney
• [Bioperl-l] WARNING INCOMING: collection consolidation   Ewan Birney
• [Bioperl-l] A picky question about "fasta.qual" files   Ewan Birney
• [Bioperl-l] problem with Bio::DB::Query::GenBank   Ewan Birney
• [Bioperl-l] Problem untarring the 1.2 distribution   Paul Boutros
• [Bioperl-l] use modules in a PC (fwd)   Paul Boutros
• [Bioperl-l] Reverse Comp Coding Puzzler   Paul Boutros
• [Bioperl-l] Blast stuff   Steve Chervitz
• [Bioperl-l] Permission denied when using Bio::SearchIO in CGI script   Marcus Claesson
• [Bioperl-l] Permission denied when using Bio::SearchIO in CGI script   Marcus Claesson
• [Bioperl-l] SeqIO/scf.pm bug (with fix)   Tony Cox
• [Bioperl-l] bioperl filehandles   Tony Cox
• [Bioperl-l] Bio::Seq::SequenceTrace and Bio::SeqIO::scf   Tony Cox
• [Bioperl-l] problem with cvs server   Allen Day
• [Bioperl-l] ActiveState Perl 5.8 and Bioperl   Chris Fields
• [Bioperl-l] Windows Bioperl 1.2   Chris Fields
• [Bioperl-l] A Bio::Graphics/Bio::Seq problem   Ed Green
• [Bioperl-l] Installation of Bioperl1.2   Eley Greg
• [Bioperl-l] Closing a SeqIO filehandle   Nancy Hansen
• [Bioperl-l] A picky question about "fasta.qual" files   Nancy Hansen
• [Bioperl-l] app to translate EST contigs   Charles Hauser
• [Bioperl-l] extracting 'species' from ncbi records   Charles Hauser
• [Bioperl-l] Problem untarring the 1.2 distribution   Tim Henderson
• [Bioperl-l] Problem untarring the 1.2 distribution   Tim Henderson
• [Bioperl-l] Problem untarring the 1.2 distribution   Tim Henderson
• [Bioperl-l] Problem untarring the 1.2 distribution   Tim Henderson
• [Bioperl-l] [Bioperl-guts-l] [Bug 1368] New: Error running standalone blast (bioperl-live) (fwd)   Shawn Hoon
• [Bioperl-l] T-Coffee and Simple Align Objectsls   Shawn Hoon
• [Bioperl-l] Bioperl error : can't locate Bio/Tool/Run/WrapperBase.pm   Shawn Hoon
• [Bioperl-l] Accessing remote databases   Hsu, Vicky
• [Bioperl-l] Installation of Bioperl   Hsu, Vicky
• [Bioperl-l] Installation of Bioperl1.2   Hsu, Vicky
• [Bioperl-l] Installation of Bioperl 1.2   Hsu, Vicky
• [Bioperl-l] Genbank/EMBL output   Alex Hudek
• [Bioperl-l] Genbank/EMBL output   Alex Hudek
• [Bioperl-l] Print alignments for several HSPs? (not for the whole report)   Vsevolod (Simon) Ilyushchenko
• [Bioperl-l] nexus to fasta converter   Amit R Indap
• [Bioperl-l] nexus to fasta converter   Amit R Indap
• [Bioperl-l] Search engine   Eric Jain
• [Bioperl-l] Genbank/EMBL output   Keith James
• [Bioperl-l] Bio::SeqIO::genbank Keywords Question   Jonathan B Joseph
• [Bioperl-l] Bio::SeqIO::genbank Keywords Question   Jonathan B Joseph
• [Bioperl-l] do not hate individual getter/setters coding?   Xiao Juguang
• [Bioperl-l] automating data analysis?   KB
• [Bioperl-l] Mapping between DNA and Protein coordinates   Arnaud Kerhornou
• [Bioperl-l] newbie: BLAST Parsing Question   E Klee
• [Bioperl-l] BPlite to parse multi query sequence report   E Klee
• [Bioperl-l] Sequence Affinity and Dimer/Hairpin formation   E Klee
• [Bioperl-l] project ideas   Ian Korf
• [Bioperl-l] Re: Searching the mailing list archives   Michal Kurowski
• [Bioperl-l] Re: Searching the mailing list archives   Michal Kurowski
• [Bioperl-l] Searching the mailing list archives   Hilmar Lapp
• [Bioperl-l] use modules in a PC   Hilmar Lapp
• [Bioperl-l] use modules in a PC   Hilmar Lapp
• [Bioperl-l] Newbie question: BIOSEQ/Geneseq?   Hilmar Lapp
• [Bioperl-l] app to translate EST contigs   Hilmar Lapp
• [Bioperl-l] Problems with DB::GenBANK and species()->common_name()   Hilmar Lapp
• [Bioperl-l] Bio::SeqIO::genbank Keywords Question   Hilmar Lapp
• [Bioperl-l] Fwd: [Bug 1365] load_seqdatabase.pl fails when LOCUS name contains a space   Hilmar Lapp
• [Bioperl-l] extracting 'species' from ncbi records   Hilmar Lapp
• [Bioperl-l] extracting 'species' from ncbi records   Hilmar Lapp
• [Bioperl-l] bond() FT operator   Hilmar Lapp
• [Bioperl-l] circular refs/ unattach_seq in SeqFeatureI   Hilmar Lapp
• [Bioperl-l] error parsing new ace files with Bio::Assembly   Hilmar Lapp
• [Bioperl-l] biolinux.org: bioperl rpm   Hilmar Lapp
• [Bioperl-l] circular refs/ unattach_seq in SeqFeatureI   Hilmar Lapp
• [Bioperl-l] Production scripts   Hilmar Lapp
• [Bioperl-l] problem with Bio::DB::Query::GenBank   Hilmar Lapp
• [Bioperl-l] WARNING INCOMING: collection consolidation   Hilmar Lapp
• [Bioperl-l] problem with Bio::DB::Query::GenBank   Hilmar Lapp
• [Bioperl-l] Problem untarring the 1.2 distribution   Heikki Lehvaslaiho
• [Bioperl-l] Bio::Graphics Question   Heikki Lehvaslaiho
• [Bioperl-l] Mapping between DNA and Protein coordinates   Heikki Lehvaslaiho
• [Bioperl-l] do not hate individual getter/setters coding?   Heikki Lehvaslaiho
• [Bioperl-l] Re: Determining strand orientation from bl2seq report   Boris Lenhard
• [Bioperl-l] Clustalw && large sequence number   Sally Li
• [Bioperl-l] Clustalw && large sequence number   Sally Li
• [Bioperl-l] Clustalw && large sequence number   Sally Li
• [Bioperl-l] (no subject)   Sally Li
• [Bioperl-l] biolinux.org: bioperl rpm   Marc Logghe
• [Bioperl-l] bioperl rpm on line   Marc Logghe
• RE: [Bioperl-l] Bio::Tools::Run::WrapperBase ?    Marc Logghe
• [Bioperl-l] Re: How to convert ABI trace file to Phred file?   Aaron J Mackey
• [Bioperl-l] Re: How to convert ABI trace file to Phred file?   Aaron J Mackey
• [Bioperl-l] bond() FT operator   Aaron J Mackey
• [Bioperl-l] project ideas   Aaron J Mackey
• [Bioperl-l] An update for my DNA Smith-Waterman code   Aaron J Mackey
• [Bioperl-l] An update for my DNA Smith-Waterman code   Aaron J Mackey
• [Bioperl-l] An update for my DNA Smith-Waterman code   Aaron J Mackey
• [Bioperl-l] An update for my DNA Smith-Waterman code   Aaron J Mackey
• [Bioperl-l] An update for my DNA Smith-Waterman code   Aaron J Mackey
• [Bioperl-l] An update for my DNA Smith-Waterman code   Aaron J Mackey
• [Bioperl-l] problem with Bio::DB::Query::GenBank   Aaron J Mackey
• [Bioperl-l] DNA Smith-Waterman code   Yee Man
• [Bioperl-l] Re: DNA Smith-Waterman code   Yee Man
• [Bioperl-l] An update for my DNA Smith-Waterman code   Yee Man
• [Bioperl-l] An update for my DNA Smith-Waterman code   Yee Man
• [Bioperl-l] An update for my DNA Smith-Waterman code   Yee Man
• [Bioperl-l] An update for my DNA Smith-Waterman code   Yee Man
• [Bioperl-l] An update for my DNA Smith-Waterman code   Yee Man
• [Bioperl-l] An update for my DNA Smith-Waterman code   Yee Man
• [Bioperl-l] An update for my DNA Smith-Waterman code   Yee Man
• [Bioperl-l] gene ontology   Ingrid Marchal
• [Bioperl-l] Bio::Graphics Question   Leonardo Marino-Ramirez
• [Bioperl-l] problem with Bio::DB::Query::GenBank   Leonardo Marino-Ramirez
• [Bioperl-l] Bio::Seq::SequenceTrace and Bio::SeqIO::scf   Chad Matsalla
• [Bioperl-l] Bio::Seq::SequenceTrace and Bio::SeqIO::scf   Chad Matsalla
• [Bioperl-l] Can't connect to www.ncbi.nih.gov:80 (Bad hostname 'www.ncbi.nih.gov')   Damien Mattei
• [Bioperl-l] Can't connect to www.ncbi.nih.gov:80 (Bad hostname'www.ncbi.nih.gov')   Damien Mattei
• [Bioperl-l] Can't connect to www.ncbi.nih.gov:80 (Bad hostname'www.ncbi.nih.gov')   Damien Mattei
• [Bioperl-l] biolinux.org: bioperl rpm   Hunter Matthews
• [Bioperl-l] Finding subject length with BPlite   Susan J. Miller
• [Bioperl-l] Problems with DB::GenBANK and species()->common_name()   Stephen Montgomery
• [Bioperl-l] Bioperl integration of mlagan/lagan   Stephen Montgomery
• [Bioperl-l] Mlagan/lagan bioperl object   Stephen Montgomery
• [Bioperl-l] Clustalw && large sequence number   Christopher J Moressi
• [Bioperl-l] getting alignments out of blast reports   Nandita Mullapudi
• Bioperl under cygwin revisited RE: [Bioperl-l] Bioperl 1.2 Releas ed   Nash, John
• [Bioperl-l] Installing bioperl 1.2 with cygwin's perl 5.6.1 and fixing the fa iled Index.t tests   Nash, John
• [Bioperl-l] Reverse Comp Coding Puzzler   David Nix
• [Bioperl-l] Thanks re Reverse Comp Coding Puzzler!   David Nix
• [Bioperl-l] error parsing new ace files with Bio::Assembly   Andy Nunberg
• Fwd: [Bioperl-l] error parsing new ace files with Bio::Assembly   Andy Nunberg
• [Bioperl-l] Errors using Bio::Assembly   Andy Nunberg
• [Bioperl-l] problems getting 1.2 tarball   Brian Osborne
• [Bioperl-l] problems getting 1.2 tarball   Brian Osborne
• [Bioperl-l] problems getting 1.2 tarball   Brian Osborne
• [Bioperl-l] Bioperl install on Windows XP   Brian Osborne
• [Bioperl-l] Re: Arrays of BioSeq and TCoffee   Brian Osborne
• [Bioperl-l] extracting 'species' from ncbi records   Brian Osborne
• [Bioperl-l] Installation of Bioperl 1.2   Brian Osborne
• [Bioperl-l] getting alignments out of blast reports   Brian Osborne
• [Bioperl-l] Production scripts   Brian Osborne
• [Bioperl-l] problems with install Bundle::Bioperl   Brian Osborne
• [Bioperl-l] Sequence Affinity and Dimer/Hairpin formation   Brian Osborne
• [Bioperl-l] problem with Bio::DB::Query::GenBank   Brian Osborne
• [Bioperl-l] Bio::DB::GenPept   Brian Osborne
• [Bioperl-l] HMMer Results   Brian Osborne
• [Bioperl-l] Can't connect to www.ncbi.nih.gov:80 (Bad hostname'www.ncbi.nih.gov')   Francis Ouellette
• [Bioperl-l] RE: FASTA Smith-Waterman (Swat) implementation   William R. Pearson
• [Bioperl-l] Genbank/EMBL output   Matthew Pocock
• [Bioperl-l] biolinux.org: bioperl rpm   Guillaume Rousse
• [Bioperl-l] getting alignments out of blast reports   Remo Sanges
• [Bioperl-l] Bio::DB::GenPept   Neil Saunders
• [Bioperl-l] problems getting 1.2 tarball   Peter Schattner
• [Bioperl-l] Bio::Tools::Run::WrapperBase ?    Peter Schattner
• [Bioperl-l] problem with Bio::DB::Query::GenBank   Prachi Shah
• [Bioperl-l] Errors using Bio::Assembly   Robson Francisco de Souza
• [Bioperl-l] SeqIO/scf.pm bug (with fix)   Jason Stajich
• [Bioperl-l] Re: Question: single out fasta format seq from .aln(Clustalw) file   Jason Stajich
• [Bioperl-l] problems getting 1.2 tarball   Jason Stajich
• [Bioperl-l] Bio::Graphics Question   Jason Stajich
• [Bioperl-l] problems getting 1.2 tarball   Jason Stajich
• [Bioperl-l] Using Bioperl BLAST with a cgi script   Jason Stajich
• [Bioperl-l] Biocorba   Jason Stajich
• [Bioperl-l] Finding subject length with BPlite   Jason Stajich
• [Bioperl-l] Print alignments for several HSPs? (not for the whole report)   Jason Stajich
• [Bioperl-l] webstuff   Jason Stajich
• [Bioperl-l] BPlite to parse multi query sequence report   Jason Stajich
• [Bioperl-l] Accessing remote databases   Jason Stajich
• [Bioperl-l] Arrays of BioSeq and TCoffee   Jason Stajich
• [Bioperl-l] extracting 'species' from ncbi records   Jason Stajich
• [Bioperl-l] Installation of Bioperl1.2   Jason Stajich
• [Bioperl-l] megablast parser   Jason Stajich
• [Bioperl-l] Can't connect to www.ncbi.nih.gov:80 (Bad hostname'www.ncbi.nih.gov')   Jason Stajich
• [Bioperl-l] do not hate individual getter/setters coding?   Jason Stajich
• [Bioperl-l] [Bioperl-guts-l] [Bug 1368] New: Error running standalone blast (bioperl-live) (fwd)   Jason Stajich
• [Bioperl-l] Installation of Bioperl 1.2   Jason Stajich
• [Bioperl-l] project ideas   Jason Stajich
• [Bioperl-l] project ideas   Jason Stajich
• [Bioperl-l] problem with cvs server   Jason Stajich
• [Bioperl-l] circular refs/ unattach_seq in SeqFeatureI   Jason Stajich
• [Bioperl-l] circular refs/ unattach_seq in SeqFeatureI   Jason Stajich
• [Bioperl-l] negative reading frames in Search/HSP/BlastHSP.pm   Jason Stajich
• [Bioperl-l] Determining strand orientation from bl2seq report   Jason Stajich
• [Bioperl-l] biolinux.org: bioperl rpm   Jason Stajich
• [Bioperl-l] circular refs/ unattach_seq in SeqFeatureI   Jason Stajich
• [Bioperl-l] Permission denied when using Bio::SearchIO in CGI script   Jason Stajich
• [Bioperl-l] circular refs/ unattach_seq in SeqFeatureI   Jason Stajich
• [Bioperl-l] Determining strand orientation from bl2seq report   Jason Stajich
• [Bioperl-l] Re: Determining strand orientation from bl2seq report   Jason Stajich
• [Bioperl-l] Blast stuff   Jason Stajich
• [Bioperl-l] Blast stuff   Jason Stajich
• [Bioperl-l] Blast stuff   Jason Stajich
• [Bioperl-l] Permission denied when using Bio::SearchIO in CGI script   Jason Stajich
• [Bioperl-l] nexus to fasta converter   Jason Stajich
• [Bioperl-l] Closing a SeqIO filehandle   Jason Stajich
• [Bioperl-l] bioperl filehandles   Jason Stajich
• [Bioperl-l] A Bio::Graphics/Bio::Seq problem   Jason Stajich
• [Bioperl-l] WARNING INCOMING: collection consolidation   Jason Stajich
• [Bioperl-l] question about $feature->add_sub_SeqFeature and Bio::Graphics   Lincoln Stein
• [Bioperl-l] Bio::Graphics Question   Lincoln Stein
• [Bioperl-l] Re: [Fwd: [Bug 1366] New: Bio::Graphics::Panel fails on call to BioSeq start() method]   Lincoln Stein
• [Bioperl-l] A Bio::Graphics/Bio::Seq problem   Lincoln Stein
• [Bioperl-l] WARNING INCOMING: collection consolidation   Lincoln Stein
• [Bioperl-l] app to translate EST contigs   Elia Stupka
• [Bioperl-l] app to translate EST contigs   Elia Stupka
• [Bioperl-l] question about $feature->add_sub_SeqFeature and Bio::Graphics   June Tantoolvesm
• [Bioperl-l] Newbie question: BIOSEQ/Geneseq?   Mayank Thanawala
• [Bioperl-l] Problem using clustalw.pl   Giuseppe Torelli
• [Bioperl-l] use modules in a PC   Tsengcrank at aol.com
• [Bioperl-l] Bio::Graphics Question   Jun Wan
• [Bioperl-l] Bio::Graphics Question   Jun Wan
• [Bioperl-l] app to translate EST contigs   Jun Wan
• [Bioperl-l] Problem using clustalw.pl   James Wasmuth
• [Bioperl-l] newbie: BLAST Parsing Question   James Wasmuth
• [Bioperl-l] Using Bioperl BLAST with a cgi script   James Wasmuth
• [Bioperl-l] Arrays of BioSeq and TCoffee   James Wasmuth
• [Bioperl-l] Re: Arrays of BioSeq and TCoffee   James Wasmuth
• [Bioperl-l] Arrays of BioSeq and TCoffee   James Wasmuth
• [Bioperl-l] Clustalw && large sequence number   James Wasmuth
• [Bioperl-l] T-Coffee and Simple Align Objects   James Wasmuth
• [Bioperl-l] getting alignments out of blast reports   James Wasmuth
• [Bioperl-l] getting alignments out of blast reports   James Wasmuth
• [Bioperl-l] nexus to fasta converter   James Wasmuth
• [Bioperl-l] nexus to fasta converter   James Wasmuth
• [Bioperl-l] HMMer Results   James Wasmuth
• [Bioperl-l] HMMer Results   James Wasmuth
• [Bioperl-l] Searching the mailing list archives   Wiepert, Mathieu
• [Bioperl-l] RE: Searching the mailing list archives   Wiepert, Mathieu
• [Bioperl-l] RE: Searching the mailing list archives   Wiepert, Mathieu
• [Bioperl-l] dbSNP, dbEST fetch by dbSNp, dbEST ID's??   Wiepert, Mathieu
• [Bioperl-l] GenBank db property?   Wiepert, Mathieu
• [Bioperl-l] Re: How to convert ABI trace file to Phred file?   Hong Xu
• [Bioperl-l] Re: How to convert ABI trace file to Phred file?   Hong Xu
• [Bioperl-l] Auto-response for your message to bioperl-bugs@bio.perl.org   bioperl-bugs-admin at bioperl.org
• [Bioperl-l] Using Bioperl BLAST with a cgi script   boileau at essi.fr
• [Bioperl-l] Using Bioperl BLAST with a cgi script   boileau at essi.fr
• [Bioperl-l] Bioperl error : can't locate Bio/Tool/Run/WrapperBase.pm   boileau at essi.fr
• [Bioperl-l] Bioperl error : can't locate Bio/Tool/Run/WrapperBase.pm   boileau at essi.fr
• [Bioperl-l] Yet another problem, with Bio::Graphics   boileau at essi.fr
• [Bioperl-l] A Bio::Graphics/Bio::Seq problem   boileau at essi.fr
• [Bioperl-l] A Bio::Graphics/Bio::Seq problem   boileau at essi.fr
• [Bioperl-l] problems with install Bundle::Bioperl   david_aaron at softhome.net
• [Bioperl-l] YAPC::Paris 23-25 July   michael
• [Bioperl-l] Finding subject length with BPlite   nkuipers
• [Bioperl-l] BPlite to parse multi query sequence report   nkuipers
• [Bioperl-l] Clustalw && large sequence number   nkuipers
• [Bioperl-l] nexus to fasta converter   nkuipers
• [Bioperl-l] Bio::Seq::SequenceTrace and Bio::SeqIO::scf   nkuipers
• [Bioperl-l] Errors using Bio::Assembly   nkuipers
• [Bioperl-l] Errors using Bio::Assembly   nkuipers
• [Bioperl-l] Reverse Comp Coding Puzzler   shawnh at fugu-sg.org
• [Bioperl-l] Bioperl install on Windows XP   li teon
• [Bioperl-l] LFASTA and bioperl   li teon
• [Bioperl-l] Bio::Tools::Run::WrapperBase ?    thierlan at freesurf.fr

Last message date: Fri Jan 31 21:47:12 EDT 2003
Archived on: Fri Jan 31 20:23:14 EDT 2003

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• More info on this list...