June 2004 Archives by thread

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Starting: Tue Jun 1 02:11:16 EST 2004
Ending: Wed Jun 30 15:06:27 EST 2004
Messages: 247

• [Bioperl-l] Bio::Seq::Meta::Array method   Remo Sanges
• [Bioperl-l] Bio::Tools::Run::Alignment::Clustalw. Alignment doesn't print out in CGI   Tariq Shafi
• [Bioperl-l] retrieving coding sequences from swissprot protein accessions   Michael Bradley
  • [Bioperl-l] retrieving coding sequences from swissprot protein accessions   Jason Stajich
• [Bioperl-l] IMGT databases   Mauricio Herrera Cuadra
• [Bioperl-l] SGD GFF3 file released   Stan Dong
  • [Bioperl-l] Re: [Gmod-schema] SGD GFF3 file released   Suzanna Lewis
• [Bioperl-l] problem with not transformed negative numbers in .soft file of GEO database   Gong Wuming
  • [Bioperl-l] problem with not transformed negative numbers in .soft file of GEO database   Sean Davis
  • [Bioperl-l] problem with not transformed negative numbers in .soft file of GEO database   Remo Sanges
• [Bioperl-l] Phylip error   Jonathan Manning
  • [Bioperl-l] Phylip error   Jason Stajich
    • [Bioperl-l] Phylip error   Jonathan Manning
      • [Bioperl-l] Phylip error   Jason Stajich
      • [Bioperl-l] Phylip error   Jonathan Manning
• [Bioperl-l] Making gff files for ucsc or ncbi build   Starr Hazard
  • [Bioperl-l] Making gff files for ucsc or ncbi build   Lincoln Stein
• [Bioperl-l] Warning message terminates Stream_by_query?   JAMES IBEN
  • [Bioperl-l] Warning message terminates Stream_by_query?   Jason Stajich
• [Bioperl-l] Biosql documentation request   Brian Osborne
  • [Bioperl-l] Biosql documentation request   Hilmar Lapp
    • [Bioperl-l] Biosql documentation request   Brian Osborne
      • [Bioperl-l] Biosql documentation request   Hilmar Lapp
      • [Bioperl-l] Biosql documentation request   Brian Osborne
      • [Bioperl-l] Biosql documentation request   Hilmar Lapp
• [Bioperl-l] downlaoding pdb files   luisa pugliese
  • [Bioperl-l] downlaoding pdb files   Jurgen Pletinckx
  • [Bioperl-l] downlaoding pdb files   S.Paul
• [Bioperl-l] downlaoding pdb files   Ian Donaldson
• [Bioperl-l] Genome Informatics meeting.   Ewan Birney
• [Bioperl-l] Getting all thae matrices from transfac   gtg974p at mail.gatech.edu
  • [Bioperl-l] Getting all thae matrices from transfac   Stefan Kirov
• [Bioperl-l] Really weird bl2seq behavior   Stefan Kirov
• [Bioperl-l] Calculating Tm for nucleotides   Sean Davis
  • [Bioperl-l] Calculating Tm for nucleotides   Rob Edwards
• [Bioperl-l] accessing genbank   S.Paul
  • [Bioperl-l] accessing genbank   Brian Osborne
  • [Bioperl-l] accessing genbank   Jason Stajich
  • [Bioperl-l] accessing genbank   S.Paul
• [Bioperl-l] Another Phylip question   Jonathan Manning
• [Bioperl-l] Blast against the mouse genome   Jonathan Manning
  • [Bioperl-l] Blast against the mouse genome   pdavid at netvisao.pt
• [Bioperl-l] doc.bioperl.org   Jason Stajich
• [Bioperl-l] Blast against the mouse genome   Jonathan Manning
  • [Bioperl-l] Blast against the mouse genome   Jason Stajich
    • [Bioperl-l] Blast against the mouse genome   Jonathan Manning
• [Bioperl-l] Getting all thae matrices from transfac   Stefan Kirov
• [Bioperl-l] Bio::AlignIO::Pfam   Tariq Shafi
  • [Bioperl-l] Bio::AlignIO::Pfam   James Thompson
• [Bioperl-l] blasting a huge amount of data   aditi gupta
• [Bioperl-l] blast   aditi gupta
• [Bioperl-l] SeqFeatureI.pm: get all starts and ends from 'join'   Jan Aerts
• [Bioperl-l] SearchIO.pm: recalculate position between hit and qry   Jan Aerts
  • [Bioperl-l] SearchIO.pm: recalculate position between hit and qry   Jason Stajich
• [Bioperl-l] SeqFeatureI.pm: get all starts and ends from 'join'   Marc Logghe
  • [Bioperl-l] SeqFeatureI.pm: get all starts and ends from 'join'   Jan Aerts
• [Bioperl-l] Sequence of Blast hit   Jonathan Manning
  • [Bioperl-l] Sequence of Blast hit   Jason Stajich
    • [Bioperl-l] Sequence of Blast hit   Jonathan Manning
  • [Bioperl-l] Sequence of Blast hit   aditi gupta
• [Bioperl-l] Sequence of Blast hit   Jonathan Manning
• [Bioperl-l] how to blast   aditi gupta
  • [Bioperl-l] how to blast   Jonathan Manning
• [Bioperl-l] amino acid sequence from a microbial gene id   jwon at ucalgary.ca
  • [Bioperl-l] amino acid sequence from a microbial gene id   Brian Osborne
• [Bioperl-l] remote blast vs standalone blast   jwon at ucalgary.ca
  • [Bioperl-l] remote blast vs standalone blast   Remo Sanges
• [Bioperl-l] unigene object from blast report   jwon at ucalgary.ca
  • [Bioperl-l] unigene object from blast report   Sean Davis
• [Bioperl-l] chromatogram/scf ----> gif/jpg/png?   Mark Johnson
• [Bioperl-l] bioperl-db   Shaul Zevin
  • [Bioperl-l] bioperl-db   Hilmar Lapp
• [Bioperl-l] Consensus with ClustalW   FERNANDA SCARIOT
  • [Bioperl-l] Consensus with ClustalW   Jason Stajich
• [Bioperl-l] object   aditi gupta
• [Bioperl-l] bsml- XML and XML::DOM?   hafiz hafiz
• [Bioperl-l] XML::DOM and bsml-Xml?   hafiz hafiz
  • [Bioperl-l] XML::DOM and bsml-Xml?   Brian Osborne
• [Bioperl-l] parsing output from an avid alignment   Jonathan Manning
  • [Bioperl-l] parsing output from an avid alignment   Brian Osborne
  • [Bioperl-l] parsing output from an avid alignment   Shawn Hoon
    • [Bioperl-l] parsing output from an avid alignment   Jonathan Manning
• [Bioperl-l] do i have to install ?   aditi gupta
  • [Bioperl-l] do i have to install ?   Brian Osborne
• [Bioperl-l] Trouble install Bioperl-Ext-1.4 & dpAlign   jany
  • [Bioperl-l] Trouble install Bioperl-Ext-1.4 & dpAlign   Aaron J. Mackey
• [Bioperl-l] few questions on TFBS   gtg974p at mail.gatech.edu
• [Bioperl-l] Bioperl-db: Added -flat_only option to find_by_query()   Hilmar Lapp
• [Bioperl-l] convert GenBank to GenPept   Qunfeng
• [Bioperl-l] new to bioperl   aditi gupta
  • [Bioperl-l] new to bioperl   Jason Stajich
• [Bioperl-l] XML::DOM ?   hafiz hafiz
  • [Bioperl-l] XML::DOM ?   Brian Osborne
• [Bioperl-l] retreive all seq of a species   Baranidharan P
• [Bioperl-l] remote data base connection error   Sadeq Zougari
  • [Bioperl-l] remote data base connection error   Sean Davis
  • [Bioperl-l] remote data base connection error   Baranidharan P
• [Bioperl-l] retreive all seq of a species   Paulo Almeida
  • [Bioperl-l] retreive all seq of a species   Mark Johnson
• [Bioperl-l] Trouble again while installing Bioperl-Ext-1.4 & dpAlign   jany
• [Bioperl-l] Re: [Gmod-gbrowse] trouble loading "0"   Lincoln Stein
• [Bioperl-l] clustalw output order   Mike Bradley
  • [Bioperl-l] clustalw output order   martin
• [Bioperl-l] ontology error   S.Paul
  • [Bioperl-l] ontology error   Hilmar Lapp
• [Bioperl-l] compiling bioperl-ext   luisa pugliese
  • [Bioperl-l] compiling bioperl-ext   Aaron J. Mackey
• [Bioperl-l] getting gi number   Sucheta Tripathy
  • [Bioperl-l] getting gi number   Jason Stajich
• [Bioperl-l] XML::DOM?   hafiz hafiz
  • [Bioperl-l] Comment Objects vs. Comment Strings   Charles Tilford
• [Bioperl-l] can't find Clustalw.pm   june tantoolvesm
• [Bioperl-l] can't find Clustalw.pm   Marc Logghe
  • [Bioperl-l] can't find Clustalw.pm   june tantoolvesm
• [Bioperl-l] help, please. newick.pm error   june tantoolvesm
  • [Bioperl-l] help, please. newick.pm error   Aaron J. Mackey
    • [Bioperl-l] help, please. newick.pm error   june tantoolvesm
    • [Bioperl-l] results of clustalw->seqboot->protdist->neighbor->consense   june tantoolvesm
• [Bioperl-l] Human Invitational Database   Sean Davis
  • [Bioperl-l] Human Invitational Database   Ewan Birney
    • Parsing XML. Was: [Bioperl-l] Human Invitational Database   Dave Howorth
• [Bioperl-l] retreive medine records for a species??   Baranidharan P
  • [Bioperl-l] retreive medine records for a species??   Brian Osborne
• [Bioperl-l] Any new tutorials or teaching materials lately?   Mark Wilkinson
• [Bioperl-l] Have problem to install bioperl, need help   Fengkai Zhang (Tony)
  • [Bioperl-l] Have problem to install bioperl, need help   Jason Stajich
    • [Bioperl-l] Have problem to install bioperl, need help   Fengkai Zhang (Tony)
      • [Bioperl-l] Have problem to install bioperl, need help   Chris Dagdigian
• [Bioperl-l] load_seqdatabase.pl does not like fasta format   Andy Hammer
  • [Bioperl-l] load_seqdatabase.pl does not like fasta format   Hilmar Lapp
• [Bioperl-l] getting data from ncbi   aditi gupta
  • [Bioperl-l] getting data from ncbi   Sean Davis
• [Bioperl-l] Display graphs   Christian Landry
  • [Bioperl-l] Display graphs   Hoebeke Mark
• [Bioperl-l] seqboot and random seeds   june tantoolvesm
  • [Bioperl-l] seqboot and random seeds   Jason Stajich
• [Bioperl-l] Fetching genbank sequences   S.Paul
• [Bioperl-l] load_seqdatabase.pl does not like fasta format   Marc Logghe
  • [Bioperl-l] load_seqdatabase.pl does not like fasta format   Andy Hammer
• [Bioperl-l] writing and parsing annotations   Danny Tuckwell
  • [Bioperl-l] writing and parsing annotations   Jason Stajich
• [Bioperl-l] clustal alignments with structural based gap penalties   Michael Bradley
• [Bioperl-l] Best Practices for Downloading/Mirroring Genbank   Karalius, Joseph
  • [Bioperl-l] Best Practices for Downloading/Mirroring Genbank   Mark Johnson
• [Bioperl-l] Installation Failed Tests   Simon Wagstaff
  • [Bioperl-l] Installation Failed Tests   Jason Stajich
• [Bioperl-l] no hits from Bio::SearchIO::hmmer if no alignments ?   Marc Logghe
• [Bioperl-l] about abiview.pm   Christian Greggio
• [Bioperl-l] parsing blat data   Charles Hauser
• [Bioperl-l] Clustal w - fixed width characters   Tariq Shafi
  • [Bioperl-l] Clustal w - fixed width characters   Josh Lauricha
• [Bioperl-l] Bio::Graphics - I am having trouble drawing protein domain topology   Allen Liu
  • [Bioperl-l] Bio::Graphics - I am having trouble drawing protein domain topology   Remo Sanges
• [Bioperl-l] Find tiling path   michael watson (IAH-C)
  • [Bioperl-l] Find tiling path   Remo Sanges
• [Bioperl-l] Find tiling path   michael watson (IAH-C)
• [Bioperl-l] Bio::Graphics - Here is the program in a better format   Janet Smith
• [Bioperl-l] Bio::Graphics - Here is the program in a better format   Allen Liu
• [Bioperl-l] Bio::Graphics - Here is the program in a better format   Crabtree, Jonathan
• [Bioperl-l] Bio::Graphics - Is there anyway of having multiple top-level glyphs overlaying each other   Allen Liu
• [Bioperl-l] EST clustering software   Scott Cain
• [Bioperl-l] Bio::Graphics - Is there anyway of having multipletop-level glyphs overlaying each other   Crabtree, Jonathan
• [Bioperl-l] clustal w gap penalties   Michael Bradley
• [Bioperl-l] fasta genbank record with gid   Pedro Antonio Reche
  • [Bioperl-l] fasta genbank record with gid   Jason Stajich
    • [Bioperl-l] fasta genbank record with gid   Pedro Antonio Reche
• [Bioperl-l] Conversion of contig coordinates to chromosome   Jonathan Manning
  • [Bioperl-l] Re: Conversion of contig coordinates to chromosome   Graham McVicker
• [Bioperl-l] FileCache.pm error   Marcelino Suzuki
  • [Bioperl-l] FileCache.pm error   Jason Stajich
    • [Bioperl-l] FileCache.pm error   Marcelino Suzuki
      • [Bioperl-l] FileCache.pm error   Jason Stajich
• [Bioperl-l] genbank to gff and vice versa   Sucheta Tripathy
  • [Bioperl-l] genbank to gff and vice versa   Jason Stajich
• [Bioperl-l] Electronic Chromosome Walking   michael watson (IAH-C)
• [Bioperl-l] Conversion of contig coordinates to chromosome   Jonathan Manning
• [Bioperl-l] genbank to gff and vice versa   Sucheta Tripathy
• [Bioperl-l] genbank to gff and vice versa   Marc Logghe
• [Bioperl-l] RE: EST Clustering software   Tristan Fiedler
• [Bioperl-l] Re: [Bioperl-guts-l] tigr to genbank   Jason Stajich
• [Bioperl-l] Re: [Bioperl-guts-l] tigr to genbank   Jason Stajich
• [Bioperl-l] ontology help   Marc Logghe
  • [Bioperl-l] ontology help   Hilmar Lapp
• [Bioperl-l] Bio::SeqIO bug   michael watson (IAH-C)
  • [Bioperl-l] Bio::SeqIO bug   Brian Osborne
  • [Bioperl-l] Bio::SeqIO bug   Hilmar Lapp
    • [Bioperl-l] Bio::SeqIO bug   Brian Osborne
      • [Bioperl-l] Bio::SeqIO bug   Hilmar Lapp
• [Bioperl-l] Bio::Tools::Run::Primer3 question   Sean Davis
  • [Bioperl-l] Bio::Tools::Run::Primer3 question   Josh Burdick
• [Bioperl-l] creating a graphic   Orvis, Joshua D. (HSC)
• [Bioperl-l] Error parsing TIGR xml   Fernan Aguero
  • [Bioperl-l] Re: Error parsing TIGR xml   Josh Lauricha
  • [Bioperl-l] Error parsing TIGR xml   Jason Stajich
  • [Bioperl-l] Error parsing TIGR xml   Simon K. Chan
• [Bioperl-l] bioperl Vista module   Jonathan Manning
• [Bioperl-l] Getting clustalw alignments in a form codeml can use   Julian M Catchen
  • [Bioperl-l] Getting clustalw alignments in a form codeml can use   Jason Stajich
• [Bioperl-l] SearchIO error   michael watson (IAH-C)
  • [Bioperl-l] SearchIO error   Jason Stajich
• [Bioperl-l] Help RemoteBlastError   Sadeq Zougari
• [Bioperl-l] Human genome BLAST limit?   Jonathan Manning
• [Bioperl-l] Cannot connect to local ODBA   Andy Hammer
  • [Bioperl-l] Cannot connect to local ODBA   Brian Osborne
    • [Bioperl-l] Cannot connect to local ODBA   Hilmar Lapp
      • [Bioperl-l] Cannot connect to local ODBA   Andy Hammer
• [Bioperl-l] ontology help   Marc Logghe
  • [Bioperl-l] ontology help   Hilmar Lapp
• [Bioperl-l] Using PSM to find TF site   Nigam Shah
  • [Bioperl-l] Using PSM to find TF site   Jason Stajich
• [Bioperl-l] pir.pm => bug   Laure.Durufle at serono.com
  • [Bioperl-l] pir.pm => bug   Heikki Lehvaslaiho
    • [Bioperl-l] pir.pm => bug   Hilmar Lapp
• [Bioperl-l] Phlip   Jonathan Manning
  • [Bioperl-l] Phlip   Jason Stajich
    • [Bioperl-l] Phlip   Jonathan Manning
• [Bioperl-l] Help on a basic EST-genomic alignment script   Edward Chuong
  • [Bioperl-l] Help on a basic EST-genomic alignment script   Jason Stajich
    • [Bioperl-l] Help on a basic EST-genomic alignment script   Edward Chuong
      • [Bioperl-l] Help on a basic EST-genomic alignment script   Edward Chuong
      • [Bioperl-l] Help on a basic EST-genomic alignment script   Jason Stajich
• [Bioperl-l] Electronic Chromosome Walking   Cook, Malcolm
• [Bioperl-l] Bio::Graphics - how to adjust height of a panel as you add more tracks?   Allen Liu
• [Bioperl-l] ontology help   Marc Logghe
• [Bioperl-l] Bio::DB::Query::GenBank errors   Jonathan Manning
  • [Bioperl-l] Bio::DB::Query::GenBank errors   Rob Edwards
• [Bioperl-l] dbSNP   Allen Day
• [Bioperl-l] Installing Bioperl   habulleef at kfshrc.edu.sa
  • [Bioperl-l] Installing Bioperl   Brian Osborne
  • [Bioperl-l] Installing Bioperl   S.Paul
• [Bioperl-l] Bioperl beginner has a problem!   Sonja Funke
  • [Bioperl-l] Bioperl beginner has a problem!   Andreas Kahari
• [Bioperl-l] Help with dependencies of Bioperl   Alberto Davila
• [Bioperl-l] parser for dnadist from the phylip package   martin
  • [Bioperl-l] parser for dnadist from the phylip package   Jason Stajich
  • [Bioperl-l] parsing GenScan result   Yanbin Yin
    • [Bioperl-l] parsing GenScan result   Jason Stajich
      • [Bioperl-l] parsing GenScan result   Brian Osborne
      • [Bioperl-l] parsing GenScan result   Yanbin Yin
• [Bioperl-l] RE: Bioperl DB successful queries   Law, Annie
• [Bioperl-l] Help with dependencies of Bioperl   Alberto Davila
• [Bioperl-l] RE installing bioperl in windows   Pablo Marin Garcia
  • [Bioperl-l] RE installing bioperl in windows   Brian Osborne
• [Bioperl-l] Help on a basic EST-genomic alignment script   Edward Chuong
  • [Bioperl-l] Help on a basic EST-genomic alignment script   Jason Stajich
• [Bioperl-l] SearchIO error   michael watson (IAH-C)
  • [Bioperl-l] SearchIO error   Jason Stajich

Last message date: Wed Jun 30 15:06:27 EST 2004
Archived on: Wed Jun 30 15:02:29 EST 2004

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