Candice Olson Bio
Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =...
Platforms: *nix
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Bio::Tools::AlignFactory is a base object for alignment factories. SYNOPSIS You wont be using this as an object, but using a dervied class like Bio::Tools::pSW Holds common Alignment Factory attributes in place.
Platforms: *nix
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Bio::MAGE::Protocol::Software - Software represents the software used. SYNOPSIS use Bio::MAGE::Protocol::Software; # creating an empty instance my $software = Bio::MAGE::Protocol::Software->new(); # creating an already populated instance my $software =...
Platforms: *nix
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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...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (142): Bio::Tree::Tree Download |
Bio::Restriction::Enzyme is a single restriction endonuclease (cuts DNA at specific locations). SYNOPSIS # set up a single restriction enzyme. This contains lots of # information about the enzyme that is generally parsed from a # rebase file and can then be read back use...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (141): Bio::Restriction::Enzyme Download |
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...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (137): Bio::DB::Flat::BDB::swissprot Download |
Bio::NEXUS::CodonsBlock is a Perl module that represents CODONS block in NEXUS file. METHODS new Title : new Usage : block_object = new Bio::NEXUS::CodonsBlock(); Function: Creates a new Bio::NEXUS::CodonsBlock object Returns : Bio::NEXUS::CodonsBlock object Args :.
Platforms: *nix
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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...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (129): Bio::AlignIO::bl2seq Download |
Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (127): Bio::Tools::CodonTable Download |
Bio::Map::CytoMap is a Bio::MapI compliant map implementation handling cytogenic bands. SYNOPSIS use Bio::Map::CytoMap; my $map = new Bio::Map::CytoMap(-name => human1, -species => $human); foreach my $marker ( @markers ) { # get a list of markers somewhere $map->add_element($marker); }...
Platforms: *nix
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Bio::ExtractNE::MakeDict is a package for creating dictionary. FUNCTIONS mkdict($input_file, $output_dictfile) This function creates named-entity dictionary. Note that $input_file is a hash. Currently, only SwissProt data is supported. mkdict({ sprot_file => "sprot", } => "sprot.dict");...
Platforms: *nix
License: Freeware | Size: 5.3 MB | Download (123): Bio::ExtractNE::MakeDict Download |
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}); $cdf->parse_from_file("foo.cdf"); # Find some fun facts about this chip type print...
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Somewhere in a jail that look like hell, you must to escape from this room, take care off there are Zombies and many fire, find the bio medical to can cross trough the fire and escape from this night matter. FPS Games
Platforms: Windows
License: Freeware | Size: 33.92 MB | Download (118): Hell's Room Download |
Bio::Graphics::Glyph::minmax is the minmax glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph is the common base class for Bio::Graphics::Glyph::graded_segments and Bio::Graphics::Glyph::xyplot. It adds an internal method named minmax() for calculating...
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Bio::Matrix::PSM::InstanceSite is a PSM site occurance. SYNOPSIS use Bio::Matrix::PSM::InstanceSite; #You can get an InstanceSite object either from a file: my ($instances,$matrix)=$SomePSMFile->parse_next; #or from memory my %params=(seq=>TATAAT, id=>"TATAbox1",...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (115): Bio::Matrix::PSM::InstanceSite Download |
Bio::Tree::NodeNHX is a Simple Tree Node with support for NHX tags. SYNOPSIS use Bio::Tree::NodeNHX; my $nodeA = new Bio::Tree::NodeNHX(); my $nodeL = new Bio::Tree::NodeNHX(); my $nodeR = new Bio::Tree::NodeNHX(); my $node = new Bio::Tree::NodeNHX(); $node->add_Descendents($nodeL);...
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Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries. SYNOPSIS use Bio::SAGE::Comparison; $sage = Bio::SAGE::Comparison->new(); This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE)...
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License: Freeware | Size: 8.19 KB | Download (110): Bio::SAGE::Comparison Download |
Bio::SeqIO::fastq is a fastq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. This object can transform Bio::Seq and Bio::Seq::SeqWithQuality objects to and from fastq flat file databases. Fastq is a file format used frequently at...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (110): Bio::SeqIO::fastq Download |
Bio::Ontology::Relationship is a relationship for an ontology. SYNOPSIS $rel = Bio::Ontology::Relationship->new( -identifier => "16847", -subject_term => $subj, -object_term => $obj, -predicate_term => $pred ); This is a basic implementation of Bio::Ontology::RelationshipI. The...
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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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