Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store River stage zero No dependents

The Bio::DB::SeqFeature object is the default SeqFeature class stored in Bio::DB::SeqFeature databases. It implements both the Bio::DB::SeqFeature::NormalizedFeatureI and Bio::DB::SeqFeature::NormalizedTableFeatureI interfaces, which means that its s...

CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC - Search in distribution

Bio::SeqFeature::Lite - Lightweight Bio::SeqFeatureI class River stage two • 60 direct dependents • 65 total dependents

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. All methods are as described in Bio::SeqFeatureI with the following additions: The new() ...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution

Bio::ToolBox::SeqFeature - Fast, simple SeqFeature implementation River stage zero No dependents

SeqFeature objects represent functional elements on a genomic or chromosomal sequence, such as genes, transcripts, exons, etc. In many cases, especially genes, they have a hierarchical structure, typically in this order gene mRNA or transcript exon C...

TJPARNELL/Bio-ToolBox-1.68 - 24 Jan 2021 19:38:27 UTC - Search in distribution

Bio::SeqFeature::Annotated - PLEASE PUT SOMETHING HERE River stage zero No dependents

None yet, complain to authors....

CJFIELDS/Bio-FeatureIO-1.6.905 - 05 Sep 2014 17:34:58 UTC - Search in distribution

FAST::Bio::SeqFeature::Generic - Generic SeqFeature River stage zero No dependents

FAST::Bio::SeqFeature::Generic is a generic implementation for the FAST::Bio::SeqFeatureI interface, providing a simple object to provide all the information for a feature on a sequence. For many Features, this is all you will need to use (for exampl...

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution

Bio::BioStudio::SeqFeature::Tag - a feature representing a PCRTag River stage zero No dependents

BioStudio functions...

NOTDOCTOR/Bio-BioStudio-2.11 - 04 Dec 2015 18:59:24 UTC - Search in distribution

Bio::DB::Persistent::SeqFeature - Proxy object for database SeqFeatureI representations River stage zero No dependents

No description yet ......

CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 UTC - Search in distribution

Bio::MAGE::BioSequence::SeqFeature - Class for the MAGE-OM API River stage zero No dependents

From the MAGE-OM documentation for the "SeqFeature" class: Represents, in general, what would be a GenBank Feature Table annotation for a sequence....

JASONS/Bio-MAGE-20030502.3 - 14 May 2007 10:56:09 UTC - Search in distribution

Bio::DB::SeqFeature::Store::LoadHelper - Internal utility for Bio::DB::SeqFeature::Store River stage zero No dependents

For internal use only...

LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC - Search in distribution

Bio::DB::Sam - Read SAM/BAM database files River stage one • 1 direct dependent • 1 total dependent

This module provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across...

LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC - Search in distribution

Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files River stage one • 1 direct dependent • 1 total dependent

This module provides a Perl interface to the HTSlib library for indexed and unindexed SAM/BAM/CRAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information a...

AVULLO/Bio-DB-HTS-3.01 - 23 Apr 2019 13:51:11 UTC - Search in distribution

Bio::DB::USeq - Read USeq archive database files River stage zero No dependents

Bio::DB::USeq is a BioPerl style adaptor for reading USeq files. USeq files are compressed, indexed data files supporting modern bioinformatic datasets, including genomic points, scores, and intervals. More information about the USeq software package...

TJPARNELL/Bio-DB-USeq-0.25 - 02 Jan 2019 19:51:06 UTC - Search in distribution

lib/Bio/Emboss/Methods.pm River stage zero No dependents

PERNST/Bio-Emboss-5.0.0.1 - 06 Sep 2007 16:28:46 UTC - Search in distribution

PrimerMap - generates a primer sequence graphical map River stage zero No dependents

This object extends the Bio::SeqFeature::Generic class to provide an object for Bio::Graphics. Uses primer starting and ending coordinates (base pairs) to generate a primer map relative to a base sequence....

HALLORAN/PrimerMap-1.3 - 06 Dec 2016 15:41:59 UTC - Search in distribution

coords2gff.pl - convert mummer coords files to gff3 format River stage zero No dependents

This script converts mummer output in coords files to gff3 formatted output....

JWB/Bio-Gonzales-0.083 - 02 Jan 2021 23:10:48 UTC - Search in distribution

Bio::DB::Das::Chado - DAS-style access to a chado database River stage zero No dependents

Bio::DB::Das::Chado allows DAS style access to a Chado database, getting SeqFeatureI-compliant BioPerl objects and allowing GBrowse to access a Chado database directly....

SCAIN/Bio-DB-Das-Chado-0.35a - 07 Apr 2015 23:02:17 UTC - Search in distribution

cx-genbank2chaos.pl.pl River stage zero No dependents

Converts a genbank file to a chaos xml file (or a collection of chaos xml files). The genbank file is 'unflattened' in order to infer the relationships between features with the -islands option set, this loops through a list of genbank-formatted file...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC - Search in distribution

Bio::Graphics - Generate GD images of Bio::Seq objects River stage one • 2 direct dependents • 2 total dependents

Please see Bio::Graphics::Panel for the full interface. Also try the script glyph_help.pl for quick help on glyphs and their options....

CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC - Search in distribution

Bio::Das::Feature - A genomic annotation River stage zero No dependents

A Bio::Das::Segment::Feature object contains information about a feature on the genome retrieve from a DAS server. Each feature -- also known as an "annotation" -- has a start and end position on the genome relative to a reference sequence, as well a...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC - Search in distribution

Bio::Network::ProteinNet - a representation of a protein interaction graph. River stage zero No dependents

A ProteinNet is a representation of a protein interaction network. Its functionality comes from the Graph module of Perl and from BioPerl, the nodes or vertices in the network are Sequence objects. Nodes A node is one or more BioPerl sequence objects...

CJFIELDS/BioPerl-Network-1.006902 - 07 Nov 2011 16:27:40 UTC - Search in distribution
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