perl-Bio-Glite-0.10-alt1.noarch.rpm


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Description

perl-Bio-Glite - G-language Genome Analysis Environment REST service interface module

Property Value
Distribution ALT Linux Sisyphus
Repository Autoimports noarch
Package name perl-Bio-Glite
Package version 0.10
Package release alt1
Package architecture noarch
Package type rpm
Installed size 30.27 KB
Download size 30.27 KB
Official Mirror ftp.altlinux.org
The G-language GAE fully supports most sequence databases.
Stored annotation information:
LOCUS
$gb->{LOCUS}->{id}              -accession number
$gb->{LOCUS}->{length}          -length of sequence
$gb->{LOCUS}->{nucleotide}      -type of sequence ex. DNA, RNA
$gb->{LOCUS}->{circular}        -1 when the genome is circular.
otherwise 0
$gb->{LOCUS}->{type}            -type of species ex. BCT, CON
$gb->{LOCUS}->{date}            -date of accession
HEADER
$gb->{HEADER}
COMMENT
$gb->{COMMENT}
FEATURE
Each FEATURE is numbered(FEATURE1 .. FEATURE1172), and is a
hash structure that contains all the keys of Genbank.
In other words,  in most cases, FEATURE$i's hash at least
contains informations listed below:
$gb->{FEATURE$i}->{start}
$gb->{FEATURE$i}->{end}
$gb->{FEATURE$i}->{direction}
$gb->{FEATURE$i}->{join}
$gb->{FEATURE$i}->{note}
$gb->{FEATURE$i}->{type}        -CDS,gene,RNA,etc.
$gb->{FEATURE$i}->{feature}     -same as $i
To analyze each FEATURE, write:
foreach my $feature ($gb->feature()){
print $gb->{$feature}->{type}, "\n";
}
In the same manner, to analyze all CDS, write:
foreach my $cds ($gb->cds()){
print $gb->{$cds}->{gene}, "\n";
}
Feature or gene information can also be accessed with CDS numbers:
$gb->{CDS$i}->{start}
or with locus_tags or gene names (for CDS, tRNA, and rRNA)
$gb->{thrL}->{start}
$gb->{b0001}->{start}
BASE COUNT
$gb->{BASE_COUNT}
SEQ
$gb->seq()              -sequence data following "ORIGIN"

Alternatives

Package Version Architecture Repository
perl-Bio-Glite - - -

Requires

Name Value
/usr/share/perl5 -
perl(Data/Dumper.pm) -
perl(LWP/UserAgent.pm) -
perl(base.pm) -
rpmlib(PayloadIsLzma) -

Provides

Name Value
perl(Bio/Glite.pm) = 0.100
perl-Bio-Glite = 0.10-alt1

Download

Type URL
Binary Package perl-Bio-Glite-0.10-alt1.noarch.rpm
Source Package perl-Bio-Glite-0.10-alt1.src.rpm

Install Howto

  1. Add the following line to /etc/apt/sources.list:
    
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    
  2. Update the package index:
    # sudo apt-get update
  3. Install perl-Bio-Glite rpm package:
    # sudo apt-get install perl-Bio-Glite

Files

Path
/usr/share/doc/perl-Bio-Glite-0.10/Changes
/usr/share/doc/perl-Bio-Glite-0.10/README
/usr/share/perl5/Bio/Glite.pm

See Also

Package Description
perl-Bio-Graphics-2.25-alt1_6.noarch.rpm Generate GD images of Bio::Seq objects
perl-Bio-Graphics-Glyph-decorated_gene-0.03-alt1.noarch.rpm perl module Bio-Graphics-Glyph-decorated_gene
perl-Bio-Grep-0.10.6-alt1.noarch.rpm Perl extension for searching in DNA and Protein sequences
perl-Bio-Grep-scripts-0.10.6-alt1.noarch.rpm Bio-Grep scripts
perl-Bio-IlluminaSAV-1.0.9706-alt2.noarch.rpm Bio::IlluminaSAV - Parse Illumina SAV files
perl-Bio-JBrowse-Store-NCList-0.1-alt1.noarch.rpm modules for formatting JSON nested containment lists for use with JBrowse
perl-Bio-KEGGI-0.1.50-alt1.noarch.rpm Module to handle KEGG genome, ko and pathway files
perl-Bio-Kmer-0.21-alt1.noarch.rpm >new("file.fastq.gz",{kmercounter=>"jellyfish",numcpus=>4});
perl-Bio-LITE-Taxonomy-0.07-alt1.noarch.rpm Lightweight and efficient taxonomic tree manager
perl-Bio-LITE-Taxonomy-NCBI-0.1-alt2.noarch.rpm Lightweight and efficient NCBI taxonomic manager
perl-Bio-LITE-Taxonomy-NCBI-Gi2taxid-0.13-alt1.noarch.rpm Mappings of NCBI GI's to Taxids fast and with very low memory footprint
perl-Bio-LITE-Taxonomy-RDP-0.03-alt1.noarch.rpm Lightweight and efficient RDP taxonomic manager
perl-Bio-Lite-0.003-alt1.noarch.rpm Lightweight and fast module with a simplified API to ease scripting in bioinformatics
perl-Bio-MAGE-20030502.3-alt1.noarch.rpm perl module Bio-MAGE
perl-Bio-MAGE-Utils-20030502.0-alt1.noarch.rpm perl module Bio-MAGE-Utils
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