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Kevin James Bio freeware
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Kevin James Bio

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Added: August 02, 2010 | Visits: 1.205

Bio::Map::MappableI Bio::Map::MappableI is an object that can be placed in a map. SYNOPSIS # get a Bio::Map::MappableI somehow my $position = $element->map_position(); # these methods will be important for building sorted lists if( $position->equals($p2) ) { # do something } elsif( $position->less_tha($p2)...



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License: Freeware Size: 4.7 MB Download (109): Bio::Map::MappableI Download

Added: April 11, 2010 | Visits: 1.008

Bio::Tree::Tree Bio::Tree::Tree is an implementation of TreeI interface. SYNOPSIS # like from a TreeIO my $treeio = new Bio::TreeIO(-format => newick, -file => treefile.dnd); my $tree = $treeio->next_tree; my @nodes = $tree->get_nodes; my $root = $tree->get_root_node; This object holds handles to Nodes...





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License: Freeware Size: 4.7 MB Download (136): Bio::Tree::Tree Download

Added: November 14, 2010 | Visits: 1.017

Bio::Factory::SequenceFactoryI Bio::Factory::SequenceFactoryI is a Perl interface that allows for generic building of sequences in factories which create sequences (like SeqIO). SYNOPSIS # do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like use Bio::Seq::SeqFactory; my...


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Added: November 02, 2010 | Visits: 1.198

Bio::LiveSeq::Translation Bio::LiveSeq::Translation is a translation class for LiveSeq. This stores informations about aminoacids translations of transcripts. The implementation is that a Translation object is the translation of a Transcript object, with different possibilities of manipulation, different coordinate...


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License: Freeware Size: 4.7 MB Download (104): Bio::LiveSeq::Translation Download

Added: March 16, 2010 | Visits: 760

Bio::Tools::Run::JavaRunner Bio::Tools::Run::JavaRunner is a Perl module that can run java programs. SYNOPSIS my $runner = Bio::Tools::Run::JavaRunner->new(-jar => $jar); $runner->run(); This module is probably incomplete. It is intended to be a wrapper for running java programs..


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License: Freeware Size: 942.08 KB Download (90): Bio::Tools::Run::JavaRunner Download

Added: April 03, 2010 | Visits: 1.150

Bio::Graphics::Glyph::cds Bio::Graphics::Glyph::cds module contains the "cds" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the...


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Added: January 06, 2010 | Visits: 1.213

Bio::Graphics::Panel 1.5.2_005 Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects. SYNOPSIS # This script parses a GenBank or EMBL file named on the command # line and produces a PNG rendering of it. Call it like this: # render.pl my_file.embl | display - use strict; use Bio::Graphics;...


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License: Freeware Size: 5.7 MB Download (93): Bio::Graphics::Panel 1.5.2_005 Download

Added: April 24, 2010 | Visits: 1.194

Bio::Graphics::Feature Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel. SYNOPSIS use Bio::Graphics::Feature; # create a simple feature with no internal structure $f = Bio::Graphics::Feature->new(-start => 1000, -stop => 2000, -type => transcript, -name => alpha-1...


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Added: February 11, 2010 | Visits: 924

Bio::DB::Flat::BDB::swissprot Bio::DB::Flat::BDB::swissprot is a swissprot adaptor for Open-bio standard BDB-indexed flat file. SYNOPSIS See Bio::DB::Flat. This module allows swissprot files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this...


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License: Freeware Size: 4.7 MB Download (130): Bio::DB::Flat::BDB::swissprot Download

Added: July 15, 2010 | Visits: 1.073

Bio::Graphics::Glyph::minmax Bio::Graphics::Glyph::minmax is the minmax glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph is the common base class for Bio::Graphics::Glyph::graded_segments and Bio::Graphics::Glyph::xyplot. It adds an internal method named minmax() for calculating...


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Added: October 26, 2010 | Visits: 1.168

Bio::Graphics::FeatureFile Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file. SYNOPSIS use Bio::Graphics::FeatureFile; my $data = Bio::Graphics::FeatureFile->new(-file => features.txt); # create a new panel and render contents of the file onto it my $panel = $data->new_panel; my...


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Added: February 25, 2010 | Visits: 853

Bio::DB::GFF::Feature Bio::DB::GFF::Feature is a relative segment identified by a feature type. Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and...


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License: Freeware Size: 4.7 MB Download (86): Bio::DB::GFF::Feature Download

Added: January 14, 2010 | Visits: 730

Bio::Biblio Bio::Biblio is a Bibliographic Query Service module. SYNOPSIS use Bio::Biblio; my $biblio = new Bio::Biblio; print $biblio->find (perl)->get_count . "n"; my $collection = $biblio->find (brazma, authors); while ( $collection->has_next ) { print $collection->get_next; } #The new()...


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Added: March 12, 2010 | Visits: 853

Bio::Graph::SimpleGraph Bio::Graph::SimpleGraph is a Perl module that can create and manipulate undirected graphs. SYNOPSIS use Bio::Graph::SimpleGraph; my $graph=new SimpleGraph; # read pairs of nodes from STDIN while (<>) { my($node1,$node2)=split; $graph->add_edge($node1,$node2); } my @nodes=graph->nodes;...


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License: Freeware Size: 5.6 MB Download (101): Bio::Graph::SimpleGraph Download

Added: April 08, 2010 | Visits: 643

Bio::ConnectDots::SimpleGraph Bio::ConnectDots::SimpleGraph is a simple, hopefully fast undirected graph package. SYNOPSIS use SimpleGraph; my $graph=new Bio::ConnectDots::SimpleGraph; # read pairs of nodes from STDIN while (<>) { my($node1,$node2)=split; $graph->add_edge($node1,$node2); } my @nodes=graph->nodes;...


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License: Freeware Size: 102.4 KB Download (87): Bio::ConnectDots::SimpleGraph Download

Added: October 05, 2010 | Visits: 913

Bio::Affymetrix::CDF Bio::Affymetrix::CDF is a Perl module to parse Affymetrix CDF files. SYNOPSIS use Bio::Affymetrix::CDF; # Parse the CDF file my $cdf=new Bio::Affymetrix::CDF({"probemode"=>0}); $cdf->parse_from_file("foo.cdf"); # Find some fun facts about this chip type print...


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License: Freeware Size: 64.51 KB Download (114): Bio::Affymetrix::CDF Download

Added: March 08, 2010 | Visits: 809

Bio::AlignIO::bl2seq Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class, as in: use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "inputfilename" , -format => bl2seq); $aln = $in->next_aln(); This object can create...


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License: Freeware Size: 4.7 MB Download (117): Bio::AlignIO::bl2seq Download

Added: August 13, 2010 | Visits: 762

Bio::AlignIO::msf Bio::AlignIO::msf is a Perl module with msf sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. This object can transform Bio::Align::AlignI objects to and from msf flat file databases. The rest of the documentation details each of...


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Added: January 26, 2010 | Visits: 1.221

Bio::GMOD::Admin::Monitor::blat Bio::GMOD::Admin::Monitor::blat is a Perl module that can monitor a BLAT server. SYNOPSIS Check the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm my $gmod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase); my $version = $gmod->live_version; Update a MOD installation...


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License: Freeware Size: 71.68 KB Download (106): Bio::GMOD::Admin::Monitor::blat Download

Added: August 01, 2010 | Visits: 923

Bio::Network::IO::dip_tab Bio::Network::IO::dip_tab is a Perl class for parsing interaction data in DIP tab-delimited format. SYNOPSIS Do not use this module directly, use Bio::Network::IO. For example: my $io = Bio::Network::IO->new(-format => dip_tab, -file => data.dip); my $network = $io->next_network; The...


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License: Freeware Size: 99.33 KB Download (90): Bio::Network::IO::dip_tab Download

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