Free bio db gff feature 1.4 software for linux

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 antitrypsin,
-desc => an enzyme inhibitor,
);

# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
-name => ABC-3,
-type => gapped_alignment,
-subtype => similarity);

# build up a gene exon by exon
$e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>exon);
$e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>exon);
$e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>exon);
$f = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>gene);

This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing.

Bio::Das::Lite is a Perl extension for the DAS (HTTP+XML) Protocol.

SYNOPSIS

use Bio::Das::Lite;
my $bdl = Bio::Das::Lite->new_from_registry({category => Chromosome});
my $results = $bdl->features(22);

SUBROUTINES/METHODS

new : Constructor
my $das = Bio::Das::Lite->new(http://das.ensembl.org/das/ensembl1834);

my $das = Bio::Das::Lite->new({
timeout => 60,
dsn => http://user:pass@das.ensembl.org/das/ensembl1834,
http_proxy => http://user:pass@webcache.local.com:3128/,
});

Options can be: dsn (optional scalar or array ref, URLs of DAS services)
timeout (optional int, HTTP fetch timeout in seconds)
http_proxy (optional scalar, web cache or proxy if not set in %ENV)
caching (optional bool, primitive caching on/off)
callback (optional code ref, callback for processed XML blocks)
registry (optional array ref containing DAS registry service URLs
defaults to http://das.sanger.ac.uk/registry/services/das)
proxy_user (optional scalar, username for authenticating forward-proxy)
proxy_pass (optional scalar, password for authenticating forward-proxy)
user_agent (optional scalar, User-Agent HTTP request header value)

new_from_registry : Constructor
Similar to new above but supports capabilities and category
in the given hashref, using them to query the DAS registry and
configuring the DSNs accordingly.

my $das = Bio::Das::Lite->new_from_registry({
capabilities => [features],
category => [Protein Sequence],
});

Options are as above, plus
capability (optional arrayref of capabilities)
category (optional arrayref of categories)

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

http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif

Attributes

The following attributes are specific to this class (however, you can also set and get all attributes defined in the parent classes):

doc_number
doc_office
doc_type
applicants type: array ref of Bio::Biblio::Providers

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 directly, but instead use it via Bio::DB::Flat.

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
# for more information and examples

# get from database
$db = Bio::DB::GenBank->new();
$seqobj = $db->get_Seq_by_acc(X78121);

# make from strings in script
$seqobj = Bio::Seq->new( -display_id => my_id,
-seq => $sequence_as_string);

# gets sequence as a string from sequence object
$seqstr = $seqobj->seq(); # actual sequence as a string
$seqstr = $seqobj->subseq(10,50); # slice in biological coordinates

# retrieves information from the sequence
# features must implement Bio::SeqFeatureI interface

@features = $seqobj->get_SeqFeatures(); # just top level
foreach my $feat ( @features ) {
print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ",
$feat->end," strand ",$feat->strand,"n";

# features retain link to underlying sequence object
print "Feature sequence is ",$feat->seq->seq(),"n"
}

# sequences may have a species

if( defined $seq->species ) {
print "Sequence is from ",$species->binomial_name," [",$species->common_name,"]n";
}

# annotation objects are Bio::AnnotationCollectionIs
$ann = $seqobj->annotation(); # annotation object

# references is one type of annotations to get. Also get
# comment and dblink. Look at Bio::AnnotationCollection for
# more information

foreach my $ref ( $ann->get_Annotations(reference) ) {
print "Reference ",$ref->title,"n";
}

# you can get truncations, translations and reverse complements, these
# all give back Bio::Seq objects themselves, though currently with no
# features transfered

my $trunc = $seqobj->trunc(100,200);
my $rev = $seqobj->revcom();

# there are many options to translate - check out the docs
my $trans = $seqobj->translate();

# these functions can be chained together

my $trans_trunc_rev = $seqobj->trunc(100,200)->revcom->translate();

A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface.

In Bioperl we have 3 main players that people are going to use frequently

Bio::PrimarySeq - just the sequence and its names, nothing else.
Bio::SeqFeatureI - a location on a sequence, potentially with a sequence
and annotation.
Bio::Seq - A sequence and a collection of sequence features
(an aggregate) with its own annotation.

Although Bioperl is not tied heavily to file formats these distinctions do map to file formats sensibly and for some bioinformaticians this might help

Bio::PrimarySeq - Fasta file of a sequence
Bio::SeqFeatureI - A single entry in an EMBL/GenBank/DDBJ feature table
Bio::Seq - A single EMBL/GenBank/DDBJ entry

By having this split we avoid a lot of nasty circular references (sequence features can hold a reference to a sequence without the sequence holding a reference to the sequence feature). See Bio::PrimarySeq and Bio::SeqFeatureI for more information.

Ian Korf really helped in the design of the Seq and SeqFeature system.

Bio::ClusterI module is a cluster Perl interface.

SYNOPSIS

# see the implementations of this interface for details but # basically
my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
-members =>[$seq1,$seq2]);
my @members = $cluster->get_members();
my @sub_members = $cluster->get_members(-species=>"homo sapiens");

This interface is the basic structure for a cluster of bioperl objects. In this case it is up to the implementer to check arguments and initialize whatever new object the implementing class is designed for.

Bio::PopGen::IO contains input individual,marker,allele information.

SYNOPSIS

use Bio::PopGen::IO;
my $io = new Bio::PopGen::IO(-format => csv,
-file => data.csv);

# Some IO might support reading in a population at a time

my @population;
while( my $ind = $io->next_individual ) {
push @population, $ind;
}

This is a generic interface to reading in population genetic data (of which there really isnt too many standard formats). This implementation makes it easy to provide your own parser for the data. You need to only implement one function next_individual. You can also implement next_population if your data has explicit information about population memberhsip for the indidviduals.