September 2005 Archives by author

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Starting: Thu Sep 1 13:33:40 EST 2005
Ending: Fri Sep 30 23:12:54 EST 2005
Messages: 204

• [Bioperl-l] Make test fails   Richard Adams
• [Bioperl-l] Re: releasing next week   Richard Adams
• [Bioperl-l] What version of EMBOSS should bioperl-run work with?   Fernan Aguero
• [Bioperl-l] FreeBSD ports   Fernan Aguero
• [Bioperl-l] Remote Blast addendum   Paulo Almeida
• [Bioperl-l] RemoteBlast - Can't call method "query_name" on an undefined value   Paulo Almeida
• [Bioperl-l] Assembly error when parsing .ace files   Wes Barris
• [Bioperl-l] Cannot guess alphabet error   Wes Barris
• [Bioperl-l] Cannot guess alphabet error   Wes Barris
• [Bioperl-l] Assembly error when parsing .ace files   Wes Barris
• [Bioperl-l] get_nof_contigs returns undef   Wes Barris
• [Bioperl-l] get_nof_contigs returns undef   Wes Barris
• [Bioperl-l] remove_Node leaves parenthesis after deleting internal leaf   Kevin Beckmann
• [Bioperl-l] pointer to pseudowise ?   Ewan Birney
• [Bioperl-l] test failures on cvs head   Scott Cain
• [Bioperl-l] RemoteBlast save_output does not handle -m8 output correctly   Paul G Cantalupo
• [Bioperl-l] RemoteBlast retrieve_blast cannot return Bio::SearchIO::blasttable   Paul G Cantalupo
• [Bioperl-l] bioperl-live CVS installation   Paul G Cantalupo
• [Bioperl-l] Bio::Tools::SeqStats count_codons   Govind Chandra
• [Bioperl-l] Wrong MSG using clustalW   Zhe Chen
• [Bioperl-l] How to assess sequencing quality with Bioperl?   Cook, Malcolm
• [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Cook, Malcolm
• [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Cook, Malcolm
• [Bioperl-l] In silico Chromosome Walking   Cook, Malcolm
• [Bioperl-l] Re: Best method for downloading 100 sequences   Mauricio Herrera Cuadra
• [Bioperl-l] FreeBSD ports   Mauricio Herrera Cuadra
• [Bioperl-l] FreeBSD ports   Mauricio Herrera Cuadra
• [Bioperl-l] <no subject>   Sean Davis
• [Bioperl-l] <no subject>   Sean Davis
• [Bioperl-l] About the location of the microRNAs   Sean Davis
• [Bioperl-l] a stupid question   Sean Davis
• [Bioperl-l] a stupid question   Sean Davis
• [Bioperl-l] HOW TO REMOTE BLAST UCSC DATABASE ?   Sean Davis
• [Bioperl-l] How to read in FASTA formatted sequence without fasta header?   Sean Davis
• [Bioperl-l] RC3 candidates   Koen van der Drift
• [Bioperl-l] flybase release 4.2 gff   Michael Eisen
• [Bioperl-l] About RNA representations in Bioperl   Christopher Fields
• [Bioperl-l] delete some nodes in a Bio::Tree   Filipe Garrett
• [Bioperl-l] Bio::Tree::Node set root_node   Filipe Garrett
• [Bioperl-l] Re: flybase release 4.2 gff   Don Gilbert
• [Bioperl-l] a stupid question   Ryan Golhar
• [Bioperl-l] How to read in FASTA formatted sequence without fasta header?   Ryan Golhar
• [Bioperl-l] How to read in FASTA formatted sequence without fastaheader?   Ryan Golhar
• [Bioperl-l] How to assess sequencing quality with Bioperl?   Nathan Haigh
• [Bioperl-l] dead link on bioperl.org   Daniel Hansen
• [Bioperl-l] finding position of every instance of a pattern in asequence   George Hartzell
• [Bioperl-l] get_nof_contigs returns undef   George Hartzell
• [Bioperl-l] get_nof_contigs returns undef   George Hartzell
• [Bioperl-l] bioperl-run 1.5.1 RC1 up   George Hartzell
• [Bioperl-l] bioperl-run 1.5.1 RC1 up   George Hartzell
• [Bioperl-l] What's DrawGram.t supposed to do?   George Hartzell
• [Bioperl-l] sanity check an update the bioperl-run's t/ProtDist.t   George Hartzell
• [Bioperl-l] pointer to pseudowise ?   George Hartzell
• [Bioperl-l] What version of EMBOSS should bioperl-run work with?   George Hartzell
• [Bioperl-l] What version of EMBOSS should bioperl-run work with?   George Hartzell
• [Bioperl-l] Yet another 'what version's supposed to work?' question?   George Hartzell
• [Bioperl-l] FreeBSD ports   George Hartzell
• [Bioperl-l] sanity check an update the bioperl-run's t/ProtDist.t   George Hartzell
• [Bioperl-l] pointer to pseudowise ?   George Hartzell
• genewise [was Re: [Bioperl-l] pointer to pseudowise ?]   George Hartzell
• [Bioperl-l] feedback on small patch for bioperl-run's t/Neighbor.t   George Hartzell
• [Bioperl-l] RC3 candidates   George Hartzell
• [Bioperl-l] Problems with circular genomes   Jim Hu
• [Bioperl-l] [Bioperl -l] Setting Sequence with nonstandard characters   Andreas Kahari
• [Bioperl-l] Best method for downloading 100 sequences   Amir Karger
• [Bioperl-l] In silico Chromosome Walking   Razi Khaja
• [Bioperl-l] entrezgene binary ASN   Stefan Kirov
• [Bioperl-l] Bio::Species validate_species_name   Stefan Kirov
• [Bioperl-l] entrezgene binary ASN   Stefan Kirov
• [Bioperl-l] Bio::Species validate_species_name   Stefan Kirov
• [Bioperl-l] Bio::Species validate_species_name   Stefan Kirov
• [Bioperl-l] <no subject>   Stefan Kirov
• [Bioperl-l] <no subject>   Stefan Kirov
• [Bioperl-l] Bioperl question - please help!!!   Stefan Kirov
• [Bioperl-l] Re: entrezgene binary ASN   Stefan Kirov
• [Bioperl-l] Parser for Geneseq and PDBfinder?   Jesper Krogh
• [Bioperl-l] Re: LocationI implementation details   Hilmar Lapp
• [Bioperl-l] Bio::Species validate_species_name   Hilmar Lapp
• [Bioperl-l] Bio::Species validate_species_name   Hilmar Lapp
• [Bioperl-l] bioperl object for GO annotation entries?   Hilmar Lapp
• [Bioperl-l] RC3 candidates   Hilmar Lapp
• [Bioperl-l] RC3 candidates   Hilmar Lapp
• [Bioperl-l] RC3 candidates   Hilmar Lapp
• [Bioperl-l] Forthcoming EMBL databank changes   Heikki Lehvaslaiho
• [Bioperl-l] affymetrix CHP XDA (version 5)   Heikki Lehvaslaiho
• [Bioperl-l] [Bioperl -l] Setting Sequence with nonstandard characters   Heikki Lehvaslaiho
• [Bioperl-l] bioperl 1.5.1 RC1 up   Heikki Lehvaslaiho
• [Bioperl-l] bioperl 1.5.1 RC1 up   Heikki Lehvaslaiho
• [Bioperl-l] get_nof_contigs returns undef   Heikki Lehvaslaiho
• [Bioperl-l] get_nof_contigs returns undef   Heikki Lehvaslaiho
• [Bioperl-l] Bio::Tools::SeqStats count_codons   Heikki Lehvaslaiho
• [Bioperl-l] Bio::Tools::SeqStats count_codons   Heikki Lehvaslaiho
• [Bioperl-l] Broken RemoteBlast fixes   Leo, Paul (NIH/NHGRI)
• [Bioperl-l] a stupid question   Leo, Paul (NIH/NHGRI)
• [Bioperl-l] How to assess sequencing quality with Bioperl?   Andrew Leung
• [Bioperl-l] How to assess sequencing quality with Bioperl?   Andrew Leung
• [Bioperl-l] <no subject>   Mingyi Liu
• [Bioperl-l] Re: entrezgene binary ASN   Mingyi Liu
• [Bioperl-l] Re: entrezgene binary ASN   Mingyi Liu
• [Bioperl-l] Re: entrezgene binary ASN   Mingyi Liu
• [Bioperl-l] finding position of every instance of a pattern in asequence   Marc Logghe
• [Bioperl-l] RE: [Gmod-gbrowse] Translation glyph   Marc Logghe
• [Bioperl-l] Issue with Bio::Index::AbstractSeq::fetch   Marc Logghe
• [Bioperl-l] Issue with Bio::Index::AbstractSeq::fetch   Marc Logghe
• [Bioperl-l] Re: [Gmod-gbrowse] Translation glyph   Aaron J. Mackey
• [Bioperl-l] bioperl 1.5.1 RC1 up   Aaron J. Mackey
• [Bioperl-l] Broken RemoteBlast fixes   Aaron J. Mackey
• [Bioperl-l] Re: [Gmod-gbrowse] Translation glyph   Aaron J. Mackey
• [Bioperl-l] RC3 candidates   Aaron J. Mackey
• [Bioperl-l] In silico Chromosome Walking   Ferdinand Marletaz
• [Bioperl-l] Bio::Search results   Barry Moore
• [Bioperl-l] Bio::Search results   Barry Moore
• [Bioperl-l] Bio::Search results   Barry Moore
• [Bioperl-l] Best method for downloading 100 sequences   Barry Moore
• [Bioperl-l] Bio::Search results   Barry Moore
• [Bioperl-l] releasing next week   Barry Moore
• [Bioperl-l] releasing next week   Barry Moore
• [Bioperl-l] query   Barry Moore
• [Bioperl-l] bioperl 1.5.1 RC1 up   Barry Moore
• [Bioperl-l] dead link on bioperl.org   Barry Moore
• [Bioperl-l] a stupid question   Barry Moore
• [Bioperl-l] Bioperl question - please help!!!   Olena Morozova
• [Bioperl-l] Bio::Search results   Sean O'Keeffe
• [Bioperl-l] Bio::Search results   Sean O'Keeffe
• [Bioperl-l] Bio::Tools::Run::TribeMCL   Sean O'Keeffe
• [Bioperl-l] problem!   Brian Osborne
• [Bioperl-l] Missing SeqIO tests - need example files   Brian Osborne
• [Bioperl-l] releasing next week   Brian Osborne
• [Bioperl-l] dead link on bioperl.org   Brian Osborne
• [Bioperl-l] bioperl 1.5.1 RC1 up   Brian Osborne
• [Bioperl-l] from protein gi number to CDS seqs.   Brian Osborne
• [Bioperl-l] FW: Bioperl question - please help!!!   Brian Osborne
• [Bioperl-l] 1.5.1 RC3 Tests   Brian Osborne
• [Bioperl-l] can't parse GenBank correctly (SeqIO or included modules)   Brian Osborne
• [Bioperl-l] PDB XML Libray   Toni Hermoso Pulido
• [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   Sachin Pundhir
• [Bioperl-l] How to read in FASTA formatted sequence without fasta header?   Richard Sucgang, PhD
• [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   CHANDAN SINGH
• [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   CHANDAN SINGH
• [Bioperl-l] entrezgene binary ASN   Michael Seewald
• [Bioperl-l] Re: entrezgene binary ASN   Michael Seewald
• [Bioperl-l] Re: entrezgene binary ASN   Michael Seewald
• [Bioperl-l] Re: entrezgene binary ASN   Michael Seewald
• [Bioperl-l] affymetrix CHP XDA (version 5)   Leonardo Kenji Shikida
• [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Guy Slater
• [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Guy Slater
• [Bioperl-l] query   Neeti Somaiya
• [Bioperl-l] RemoteBlast save_output does not handle -m8 output correctly   Jason Stajich
• [Bioperl-l] methods, etc. for Bio::SearchIO on exonerate output   Jason Stajich
• [Bioperl-l] Fwd: BIoPerl and user complaints.   Jason Stajich
• [Bioperl-l] delete some nodes in a Bio::Tree   Jason Stajich
• [Bioperl-l] LocationI implementation details   Jason Stajich
• [Bioperl-l] releasing next week   Jason Stajich
• [Bioperl-l] Bio::SearchDist problem   Jason Stajich
• [Bioperl-l] test failures on cvs head   Jason Stajich
• [Bioperl-l] Re: [Bioperl-guts-l] BioPerl 1.5 fasta.pm->next_seq() fails on sequence   Jason Stajich
• [Bioperl-l] Bio::Tree::Node set root_node   Jason Stajich
• [Bioperl-l] RemoteBlast retrieve_blast cannot return Bio::SearchIO::blasttable   Jason Stajich
• [Bioperl-l] Bio::Tree method - FixedTopo tree factory with random branchlengths   Jason Stajich
• [Bioperl-l] [Bioperl -l] Setting Sequence with nonstandard characters   Jason Stajich
• [Bioperl-l] overwriting results in bl2seq report   Jason Stajich
• [Bioperl-l] bioperl 1.5.1 RC1 up   Jason Stajich
• [Bioperl-l] bioperl 1.5.1 RC1 up   Jason Stajich
• [Bioperl-l] Broken RemoteBlast fixes   Jason Stajich
• [Bioperl-l] Assembly error when parsing .ace files   Jason Stajich
• [Bioperl-l] Bio::Tools::Run::TribeMCL   Jason Stajich
• [Bioperl-l] Cannot guess alphabet error   Jason Stajich
• [Bioperl-l] Cannot guess alphabet error   Jason Stajich
• [Bioperl-l] bioperl-run 1.5.1 RC1 up   Jason Stajich
• [Bioperl-l] RemoteBlast by Bio::Perl Through proxy   Jason Stajich
• [Bioperl-l] bioperl-run 1.5.1 RC1 up   Jason Stajich
• [Bioperl-l] What version of EMBOSS should bioperl-run work with?   Jason Stajich
• [Bioperl-l] Yet another 'what version's supposed to work?' question?   Jason Stajich
• [Bioperl-l] RC3 candidates   Jason Stajich
• [Bioperl-l] remove_Node leaves parenthesis after deleting internal leaf   Jason Stajich
• [Bioperl-l] sanity check an update the bioperl-run's t/ProtDist.t   Jason Stajich
• [Bioperl-l] feedback on small patch for bioperl-run's t/Neighbor.t   Jason Stajich
• genewise [was Re: [Bioperl-l] pointer to pseudowise ?]   Jason Stajich
• [Bioperl-l] protdist changes   Jason Stajich
• [Bioperl-l] RC3 candidates   Jason Stajich
• [Bioperl-l] RC3 candidates   Jason Stajich
• [Bioperl-l] How to read in FASTA formatted sequence without fastaheader?   Jason Stajich
• [Bioperl-l] finding position of every instance of a pattern in a sequence   Andrew Stewart
• [Bioperl-l] from protein gi number to CDS seqs.   Sun, Jian
• [Bioperl-l] Bio::SearchDist problem   Gabor Toth
• [Bioperl-l] overwriting results in bl2seq report   Usha
• [Bioperl-l] Bio::Tools::Run::TribeMCL   Albert Vilella
• [Bioperl-l] Bio::Tree method - FixedTopo tree factory with random branchlengths   Albert Vilella
• [Bioperl-l] bioperl object for GO annotation entries?   Albert Vilella
• [Bioperl-l] bioperl object for GO annotation entries?   Albert Vilella
• [Bioperl-l] [Bioperl -l] Setting Sequence with nonstandard characters   Iain Wallace
• [Bioperl-l] [Bioperl -l] Setting Sequence with nonstandard characters   Iain Wallace
• [Bioperl-l] How to assess sequencing quality with Bioperl?   Andrew Walsh
• [Bioperl-l] Re: Best method for downloading 100 sequences   James Wasmuth
• [Bioperl-l] HOW TO REMOTE BLAST UCSC DATABASE ?   Ping Yao
• [Bioperl-l] About the location of the microRNAs   Alex Zhang
• [Bioperl-l] Seek advice on programming of miRNA problem   Alex Zhang
• [Bioperl-l] TreeIO nexus file parsing issue (bug?)   kevin liu
• [Bioperl-l] Remote Blast Failing   paul.boutros at utoronto.ca
• [Bioperl-l] 1.5.1 RC3 Tests   paul.boutros at utoronto.ca
• [Bioperl-l] can't parse GenBank correctly (SeqIO or included modules)   t-nakazato at muj.biglobe.ne.jp
• [Bioperl-l] problem!   thechans at citiz.net
• [Bioperl-l] a stupid question   xuying
• [Bioperl-l] a stupid question   xuying

Last message date: Fri Sep 30 23:12:54 EST 2005
Archived on: Fri Sep 30 23:29:45 EST 2005

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