lang.perl.bio.general (thread)

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