Colin Farrell Bio Imdb

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()...

Bio::Tools::Run::PiseApplication::consensus is a Perl module. Bioperl class for: CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo) References: G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein...

Bio::Index::Swissprot is a Perl Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). SYNOPSIS # Complete code for making an index for several # Swissprot files use Bio::Index::Swissprot; use strict; my $Index_File_Name = shift; my $inx =...


Platforms: *nix

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...


Platforms: *nix

Bio::Graphics::Glyph::alignment is the "alignment" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This is identical to the "graded_segments" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is...


Platforms: *nix

Bio::NEXUS::HistoryBlock is a Perl module that represents a HISTORY block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::HistoryBlock(history, $block, $verbose); This is a class representing a history block in NEXUS file METHODS new Title : new Usage : block_object = new...


Platforms: *nix

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;...


Platforms: *nix

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...


Platforms: *nix

Bio::Phylo::Manual is a Perl module that contains a Bio::Phylo v.0.14 user guide. This is the manual for Bio::Phylo. Bio::Phylo is a perl5 package for phylogenetic analysis. For installation instructions, read the README file in the root directory of the distribution. The stable URL for the...


Platforms: *nix

Bio::NEXUS::Node is a Perl module that provides functions for manipulating nodes in trees. SYNOPSIS new Bio::NEXUS::Node; METHODS new Title : new Usage : $node = new Bio::NEXUS::Node(); Function: Creates a new Bio::NEXUS::Node object Returns : Bio::NEXUS::Node object Args : none...


Platforms: *nix

Bio::ConnectDots::ConnectDots is a top level class for connect-the-dots. SYNOPSIS use Bio::ConnectDots::DB; use Bio::ConnectDots::ConnectDots; my $db=new Bio::ConnectDots::DB(-database=>test, -host=>computername, -user=>usename, -password=>secret); my $cd=my $cd=new...


Platforms: *nix

Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #...


Platforms: *nix

Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods. A workflow is defined by a set of methods which all instanciate the class PiseApplication. SYNOPSIS # First, create a Bio::Tools::Run::AnalysisFactory::Pise object: my $factory = new...


Platforms: *nix

Bio::NEXUS::Block is a Perl module that provides useful functions for blocks in NEXUS file (parent class). SYNOPSIS This module is the super class of all NEXUS block classes. It is not used specifically from a program; in other words, you dont create a new Bio::NEXUS::Block object. Other...


Platforms: *nix

Bio::Factory::SeqAnalysisParserFactoryI is a Perl interface describing objects capable of creating SeqAnalysisParserI compliant parsers. SYNOPSIS # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object...


Platforms: *nix

Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s). SYNOPSIS use strict; use Bio::Index::Blast; my ($indexfile,$file1, $file2); my $index = new Bio::Index::Blast(-filename => $indexfile, -write_flag => 1);...


Platforms: *nix

Bio::Phylo::IO Perl module contains input and output of phylogenetic data. SYNOPSIS use Bio::Phylo::IO; # parsing a tree from a newick string my $tree_string = (((A,B),C),D);; my $tree = Bio::Phylo::IO->parse( -string => $tree_string, # old parser, always adds node labels -format =>...


Platforms: *nix

Bio::Biblio::Patent is a representation of a patent. SYNOPSIS $obj = new Bio::Biblio::Patent (-doc_number => 1-2-3-4-5); #--- OR --- $obj = new Bio::Biblio::Patent; $obj->doc_number (1-2-3-4-5); A storage object for a patent. See its place in the class hierarchy in...


Platforms: *nix

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..


Platforms: *nix

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...


Platforms: *nix