lang.perl.bio.general (date)

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lang.perl.bio.general (date)

January 31, 2003

RE: Errors using Bio::Assembly, Robson Francisco de Souza
Bioperl integration of mlagan/lagan, Stephen Montgomery
RE: Errors using Bio::Assembly, nkuipers
RE: Errors using Bio::Assembly, nkuipers
Re: problem with Bio::DB::Query::GenBank, Ewan Birney
Errors using Bio::Assembly, Andy Nunberg
Re: HMMer Results, James Wasmuth
RE: HMMer Results, Brian Osborne
HMMer Results, James Wasmuth
Re: problem with Bio::DB::Query::GenBank, Hilmar Lapp
gene ontology, Ingrid Marchal
Re: problem with Bio::DB::Query::GenBank, Aaron J Mackey
Re: WARNING INCOMING: collection consolidation, Jason Stajich
RE: Bio::DB::GenPept, Brian Osborne
Re: A picky question about "fasta.qual" files, Ewan Birney
Re: WARNING INCOMING: collection consolidation, Ewan Birney
Re: problem with Bio::DB::Query::GenBank, Ewan Birney
Re: WARNING INCOMING: collection consolidation, Hilmar Lapp
Bio::DB::GenPept, Neil Saunders

January 30, 2003

A picky question about "fasta.qual" files, Nancy Hansen
WARNING INCOMING: collection consolidation, Lincoln Stein
Re: problem with Bio::DB::Query::GenBank, Hilmar Lapp
RE: problem with Bio::DB::Query::GenBank, Brian Osborne
RE: A Bio::Graphics/Bio::Seq problem, Ed Green
RE: problem with Bio::DB::Query::GenBank, Leonardo Marino-Ramirez
problem with Bio::DB::Query::GenBank, Prachi Shah
Re: A Bio::Graphics/Bio::Seq problem, Lincoln Stein
Re: A Bio::Graphics/Bio::Seq problem, boileau
Re: A Bio::Graphics/Bio::Seq problem, Jason Stajich
A Bio::Graphics/Bio::Seq problem, boileau
RE: Sequence Affinity and Dimer/Hairpin formation, Brian Osborne

January 29, 2003

Bio::Seq::SequenceTrace and Bio::SeqIO::scf, Chad Matsalla
Sequence Affinity and Dimer/Hairpin formation, E Klee
RE: problems with install Bundle::Bioperl, Brian Osborne
problems with install Bundle::Bioperl, david_aaron
RE: Bio::Seq::SequenceTrace and Bio::SeqIO::scf, nkuipers
Re: bioperl filehandles, Jason Stajich

January 28, 2003

Bio::Seq::SequenceTrace and Bio::SeqIO::scf, Chad Matsalla
Re: An update for my DNA Smith-Waterman code, Aaron J Mackey
Re: An update for my DNA Smith-Waterman code, Yee Man
Re: Bio::Tools::Run::WrapperBase ? , Peter Schattner
bioperl filehandles, Tony Cox
Re: An update for my DNA Smith-Waterman code, Aaron J Mackey
RE: [Bioperl-l] Bio::Tools::Run::WrapperBase ? , Marc Logghe
Bio::Tools::Run::WrapperBase ? , thierlan

January 27, 2003

Re: nexus to fasta converter, James Wasmuth
Re: Blast stuff, Steve Chervitz
Re: nexus to fasta converter, Amit R Indap
bioperl rpm on line, Marc Logghe
Re: nexus to fasta converter, James Wasmuth
Re: Closing a SeqIO filehandle, Jason Stajich
Closing a SeqIO filehandle, Nancy Hansen
Re: nexus to fasta converter, Jason Stajich
RE: nexus to fasta converter, nkuipers
Re: An update for my DNA Smith-Waterman code, Yee Man
Re: An update for my DNA Smith-Waterman code, Aaron J Mackey
Re: Production scripts, Hilmar Lapp
Re: An update for my DNA Smith-Waterman code, Yee Man
nexus to fasta converter, Amit R Indap
RE: getting alignments out of blast reports, Brian Osborne
Re: Production scripts, Ewan Birney
RE: FASTA Smith-Waterman (Swat) implementation, William R. Pearson
Production scripts, Brian Osborne
Re: Permission denied when using Bio::SearchIO in CGI script, Jason Stajich
Re: Blast stuff, Jason Stajich
Re: Permission denied when using Bio::SearchIO in CGI script, Marcus Claesson
YAPC::Paris 23-25 July, michael

January 26, 2003

Re: Blast stuff, Jason Stajich
Re: Blast stuff, Jason Stajich
Re: An update for my DNA Smith-Waterman code, Yee Man
Re: An update for my DNA Smith-Waterman code, Aaron J Mackey
Re: An update for my DNA Smith-Waterman code, Yee Man
Re: An update for my DNA Smith-Waterman code, Ewan Birney
Re: An update for my DNA Smith-Waterman code, Aaron J Mackey
Re: An update for my DNA Smith-Waterman code, Yee Man
Re: An update for my DNA Smith-Waterman code, Aaron J Mackey
An update for my DNA Smith-Waterman code, Yee Man

January 25, 2003

Re: Re: Determining strand orientation from bl2seq report, Jason Stajich
Re: Determining strand orientation from bl2seq report, Boris Lenhard
Re: biolinux.org: bioperl rpm, Guillaume Rousse
Re: Determining strand orientation from bl2seq report, Jason Stajich
Re: getting alignments out of blast reports, Remo Sanges

January 24, 2003

Re: getting alignments out of blast reports, James Wasmuth
Re: getting alignments out of blast reports, James Wasmuth
Re: Determining strand orientation from bl2seq report, Dave Arenillas
getting alignments out of blast reports, Nandita Mullapudi
Re: Determining strand orientation from bl2seq report, Dave Arenillas
Re: circular refs/ unattach_seq in SeqFeatureI, Hilmar Lapp
Re: biolinux.org: bioperl rpm, Hilmar Lapp
Re: error parsing new ace files with Bio::Assembly, Hilmar Lapp
Re: biolinux.org: bioperl rpm, Hunter Matthews
Re: circular refs/ unattach_seq in SeqFeatureI, Jason Stajich
Re: circular refs/ unattach_seq in SeqFeatureI, Jason Stajich
Re: Permission denied when using Bio::SearchIO in CGI script, Ewan Birney
Re: biolinux.org: bioperl rpm, Ewan Birney
Re: circular refs/ unattach_seq in SeqFeatureI, Ewan Birney
Re: Permission denied when using Bio::SearchIO in CGI script, Jason Stajich
Permission denied when using Bio::SearchIO in CGI script, Marcus Claesson
Fwd: error parsing new ace files with Bio::Assembly, Andy Nunberg
Re: circular refs/ unattach_seq in SeqFeatureI, Jason Stajich
Re: biolinux.org: bioperl rpm, Jason Stajich
Re: Determining strand orientation from bl2seq report, Jason Stajich
Re: negative reading frames in Search/HSP/BlastHSP.pm, Jason Stajich
Yet another problem, with Bio::Graphics, boileau
biolinux.org: bioperl rpm, Marc Logghe
Re: Bioperl error : can't locate Bio/Tool/Run/WrapperBase.pm, Ewan Birney
Re: Bioperl error : can't locate Bio/Tool/Run/WrapperBase.pm, boileau
Re: Bioperl error : can't locate Bio/Tool/Run/WrapperBase.pm, Shawn Hoon
Bioperl error : can't locate Bio/Tool/Run/WrapperBase.pm, boileau
Re: circular refs/ unattach_seq in SeqFeatureI, Ewan Birney
Re: Determining strand orientation from bl2seq report, Ewan Birney
negative reading frames in Search/HSP/BlastHSP.pm, Benjamin Berman
Re: circular refs/ unattach_seq in SeqFeatureI, Hilmar Lapp
circular refs/ unattach_seq in SeqFeatureI, Jason Stajich
Determining strand orientation from bl2seq report, Dave Arenillas

January 22, 2003

Re: problem with cvs server, Jason Stajich
error parsing new ace files with Bio::Assembly, Andy Nunberg
Re: problem with cvs server, Benjamin Berman
Re: project ideas, Ian Korf

January 21, 2003

Re: bond() FT operator, Hilmar Lapp
Re: project ideas, Jason Stajich
Re: project ideas, Aaron J Mackey
project ideas, Jason Stajich
RE: Installation of Bioperl 1.2, Brian Osborne
Re: T-Coffee and Simple Align Objectsls, Shawn Hoon
Re: Installation of Bioperl 1.2, Jason Stajich
Installation of Bioperl 1.2, Hsu, Vicky
Re: Can't connect to www.ncbi.nih.gov:80 (Bad hostname'www.ncbi.nih.gov'), Damien Mattei
T-Coffee and Simple Align Objects, James Wasmuth
Re: [Bioperl-guts-l] [Bug 1368] New: Error running standalone blast (bioperl-live) (fwd), Shawn Hoon
[Bioperl-guts-l] [Bug 1368] New: Error running standalone blast (bioperl-live) (fwd), Jason Stajich

January 20, 2003

Re: problem with cvs server, Allen Day
problem with cvs server, Benjamin Berman
bond() FT operator, Aaron J Mackey
Re: do not hate individual getter/setters coding?, Heikki Lehvaslaiho
Re: do not hate individual getter/setters coding?, Jason Stajich
Re: Can't connect to www.ncbi.nih.gov:80 (Bad hostname'www.ncbi.nih.gov'), Jason Stajich
LFASTA and bioperl, li teon
Re: Can't connect to www.ncbi.nih.gov:80 (Bad hostname'www.ncbi.nih.gov'), Damien Mattei
Re: Can't connect to www.ncbi.nih.gov:80 (Bad hostname'www.ncbi.nih.gov'), Francis Ouellette
Can't connect to www.ncbi.nih.gov:80 (Bad hostname 'www.ncbi.nih.gov'), Damien Mattei
Re: Genbank/EMBL output, Alex Hudek

January 19, 2003

automating data analysis?, KB
Search engine, Eric Jain

January 18, 2003

Re: Genbank/EMBL output, Ewan Birney
Re: Installation of Bioperl, Ewan Birney
Re: Genbank/EMBL output, Ewan Birney

January 17, 2003

Re: extracting 'species' from ncbi records, Hilmar Lapp
Re: extracting 'species' from ncbi records, Hilmar Lapp
(no subject), Sally Li
Re: Genbank/EMBL output, Alex Hudek
megablast parser, Jason Stajich
Re: Installation of Bioperl1.2, Jason Stajich
Re: Installation of Bioperl1.2, Eley Greg
Installation of Bioperl1.2, Hsu, Vicky
Installation of Bioperl, Hsu, Vicky
RE: extracting 'species' from ncbi records, Brian Osborne
Re: extracting 'species' from ncbi records, Jason Stajich
extracting 'species' from ncbi records, Charles Hauser
Re: Genbank/EMBL output, Keith James
Re: Genbank/EMBL output, Matthew Pocock
RE: Clustalw && large sequence number, nkuipers
Auto-response for your message to bioperl-bugs@xxxxxxxxxxxx, bioperl-bugs-admin
Clustalw && large sequence number, Sally Li
RE: Clustalw && large sequence number, Sally Li

January 16, 2003

Re: Clustalw && large sequence number, James Wasmuth
RE: Clustalw && large sequence number, Christopher J Moressi
Clustalw && large sequence number, Sally Li
Re: [Fwd: [Bug 1366] New: Bio::Graphics::Panel fails on call to BioSeq start() method], Lincoln Stein
Re: Arrays of BioSeq and TCoffee, James Wasmuth
RE: Re: Arrays of BioSeq and TCoffee, Brian Osborne
Re: Arrays of BioSeq and TCoffee, Jason Stajich
Re: Arrays of BioSeq and TCoffee, James Wasmuth
Arrays of BioSeq and TCoffee, James Wasmuth

January 15, 2003

Fwd: [Bug 1365] load_seqdatabase.pl fails when LOCUS name contains a space, Hilmar Lapp
Re: Accessing remote databases, Jason Stajich
Accessing remote databases, Hsu, Vicky
GenBank db property?, Wiepert, Mathieu
Re: Bio::SeqIO::genbank Keywords Question, Jonathan B Joseph
Re: Bio::SeqIO::genbank Keywords Question, Hilmar Lapp
do not hate individual getter/setters coding?, Xiao Juguang

January 14, 2003

RE: BPlite to parse multi query sequence report, nkuipers
Re: BPlite to parse multi query sequence report, Jason Stajich
BPlite to parse multi query sequence report, E Klee
Bio::SeqIO::genbank Keywords Question, Jonathan B Joseph
Re: Mapping between DNA and Protein coordinates, Heikki Lehvaslaiho
RE: Bioperl install on Windows XP, Brian Osborne
Mapping between DNA and Protein coordinates, Arnaud Kerhornou
Re: Problems with DB::GenBANK and species()->common_name(), Hilmar Lapp
Thanks re Reverse Comp Coding Puzzler!, David Nix
Problems with DB::GenBANK and species()->common_name(), Stephen Montgomery
Bioperl install on Windows XP, li teon

January 13, 2003

Re: Reverse Comp Coding Puzzler, Paul Boutros
RE: Reverse Comp Coding Puzzler, Jamie Hatfield \(AGCoL\)
Re: Reverse Comp Coding Puzzler, shawnh
Re: DNA Smith-Waterman code, Yee Man
Reverse Comp Coding Puzzler, David Nix

January 12, 2003

DNA Smith-Waterman code, Yee Man
Re: DNA Smith-Waterman code, Ewan Birney
Windows Bioperl 1.2, Chris Fields
ActiveState Perl 5.8 and Bioperl, Chris Fields
Re: bioperl-1.2 : man pages?, Fernan Aguero

January 11, 2003

Re: webstuff, Ewan Birney
webstuff, Jason Stajich

January 10, 2003

Re: Print alignments for several HSPs? (not for the whole report), Jason Stajich
Print alignments for several HSPs? (not for the whole report), Vsevolod (Simon) Ilyushchenko
RE: Finding subject length with BPlite, Jason Stajich
RE: Finding subject length with BPlite, nkuipers
Finding subject length with BPlite, Susan J. Miller
Re: Biocorba, Jason Stajich
Biocorba, Nils Höglund
Re: Using Bioperl BLAST with a cgi script, boileau
Re: Using Bioperl BLAST with a cgi script, James Wasmuth
Re: Using Bioperl BLAST with a cgi script, Jason Stajich
Using Bioperl BLAST with a cgi script, boileau
RE: problems getting 1.2 tarball, Brian Osborne
Re: app to translate EST contigs, Hilmar Lapp
Re: app to translate EST contigs, Elia Stupka
Re: app to translate EST contigs, Elia Stupka
Re: problems getting 1.2 tarball, Peter Schattner

January 09, 2003

Re: newbie: BLAST Parsing Question, James Wasmuth
newbie: BLAST Parsing Question, E Klee
Re: app to translate EST contigs, Jun Wan
RE: problems getting 1.2 tarball, Ewan Birney
app to translate EST contigs, Charles Hauser
RE: problems getting 1.2 tarball, Jason Stajich
RE: problems getting 1.2 tarball, Brian Osborne
Re: bioperl-1.2 : man pages?, Ewan Birney
Re: Problem using clustalw.pl, James Wasmuth
dbSNP, dbEST fetch by dbSNp, dbEST ID's??, Wiepert, Mathieu
Re: bioperl-1.2 : man pages?, Fernan Aguero
Problem using clustalw.pl, Giuseppe Torelli
Re: bioperl-1.2 : man pages?, Ewan Birney
RE: problems getting 1.2 tarball, Ewan Birney

January 08, 2003

bioperl-1.2 : man pages?, Fernan Aguero
RE: problems getting 1.2 tarball, Brian Osborne

January 07, 2003

Re: Bio::Graphics Question, Lincoln Stein
Re: Bio::Graphics Question, Jason Stajich
RE: Bio::Graphics Question, Leonardo Marino-Ramirez
Re: Bio::Graphics Question, Jun Wan
Re: problems getting 1.2 tarball, Jason Stajich
problems getting 1.2 tarball, Fernan Aguero
Re: Bio::Graphics Question, Heikki Lehvaslaiho
Bio::Graphics Question, Jun Wan

January 06, 2003

Re: Newbie question: BIOSEQ/Geneseq?, Hilmar Lapp
Newbie question: BIOSEQ/Geneseq?, Mayank Thanawala
Re: How to convert ABI trace file to Phred file?, Hong Xu
Re: How to convert ABI trace file to Phred file?, Aaron J Mackey
Re: How to convert ABI trace file to Phred file?, Hong Xu
Re: How to convert ABI trace file to Phred file?, Aaron J Mackey
Re: question about $feature->add_sub_SeqFeature and Bio::Graphics, Lincoln Stein
question about $feature->add_sub_SeqFeature and Bio::Graphics, June Tantoolvesm

January 05, 2003

Re: Question: single out fasta format seq from .aln(Clustalw) file, Jason Stajich

January 04, 2003

Re: SeqIO/scf.pm bug (with fix), Jason Stajich

January 03, 2003

Re: use modules in a PC (fwd), Paul Boutros
RE: Searching the mailing list archives, Wiepert, Mathieu
Re: Searching the mailing list archives, Michal Kurowski
RE: Searching the mailing list archives, Wiepert, Mathieu
Re: SeqIO/scf.pm bug (with fix), Tony Cox
Installing bioperl 1.2 with cygwin's perl 5.6.1 and fixing the fa iled Index.t tests, Nash, John

January 02, 2003

Re: Searching the mailing list archives, Michal Kurowski
RE: Searching the mailing list archives, Wiepert, Mathieu
Re: Problem untarring the 1.2 distribution, Tim Henderson
Re: Problem untarring the 1.2 distribution, Tim Henderson
Re: use modules in a PC, Hilmar Lapp
Re: use modules in a PC, Hilmar Lapp
Re: Problem untarring the 1.2 distribution, Heikki Lehvaslaiho
Re: Problem untarring the 1.2 distribution, Tim Henderson
use modules in a PC, Tsengcrank
Re: Problem untarring the 1.2 distribution, Paul Boutros
Problem untarring the 1.2 distribution, Tim Henderson

January 01, 2003

Bioperl under cygwin revisited RE: Bioperl 1.2 Releas ed, Nash, John
Re: Searching the mailing list archives, Hilmar Lapp

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