Search results for "module:Bio::DB::GFF::Feature"
Bio::DB::GFF::Feature - 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 its ancestors. It also inherit...
CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC
Bio::DB::GFF - Storage and retrieval of sequence annotation data
Bio::DB::GFF provides fast indexed access to a sequence annotation database. It supports multiple database types (ACeDB, relational), and multiple schemas through a system of adaptors and aggregators. The following operations are supported by this mo...
CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC
Bio::DB::GFF::Adaptor::berkeleydb - Bio::DB::GFF database adaptor for in-memory databases
This adaptor implements a berkeleydb-indexed version of Bio::DB::GFF. It requires the DB_File and Storable modules. It can be used to store and retrieve short to medium-length GFF files of several million features in length....
CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC
Bio::DB::GFF::Adaptor::memory::feature_serializer - utility methods for serializing and deserializing GFF features
CJFIELDS/Bio-DB-GFF-1.7.4
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08 Jan 2020 20:41:58 UTC
Bio::DB::SeqFeature::Store::GFF3Loader - GFF3 file loader for Bio::DB::SeqFeature::Store
The Bio::DB::SeqFeature::Store::GFF3Loader object parsers GFF3-format sequence annotation files and loads Bio::DB::SeqFeature::Store databases. For certain combinations of SeqFeature classes and SeqFeature::Store databases it features a "fast load" m...
CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC
Bio::DB::SeqFeature::Store::GFF2Loader - GFF2 file loader for Bio::DB::SeqFeature::Store
The Bio::DB::SeqFeature::Store::GFF2Loader object parsers GFF2-format sequence annotation files and loads Bio::DB::SeqFeature::Store databases. For certain combinations of SeqFeature classes and SeqFeature::Store databases it features a "fast load" m...
CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC
Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser
This class provides a simple GFF parser and writer. In the sense of a SeqAnalysisParser, it parses an input file or stream into SeqFeatureI objects, but is not in any way specific to a particular analysis program and the output that program produces....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Das - Interface to Distributed Annotation System
Bio::Das provides access to genome sequencing and annotation databases that export their data in Distributed Annotation System (DAS) format version 1.5. This system is described at http://biodas.org. Both unencrypted (http:) and SSL-encrypted (https:...
LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC
Bio::Seq - Sequence object, with features
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::Prim...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store
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
Bio::SeqFeatureI - Abstract interface of a Sequence Feature
This interface is the functions one can expect for any Sequence Feature, whatever its implementation or whether it is a more complex type (eg, a Gene). This object does not actually provide any implementation, it just provides the definitions of what...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::ToolBox - Tools for querying and analysis of genomic data
The Bio::ToolBox libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined ...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::Graphics - Generate GD images of Bio::Seq objects
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
Bio::DB::USeq - Read USeq archive database files
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-0.26 - 24 Sep 2022 02:31:45 UTC
Bio::DB::GFF::Featname - The name of a feature
Bio::DB::GFF::Featname is the name of a feature. It contains two fields: name and class. It is typically used by the Bio::DB::GFF module to denote a group, and is accepted by Bio::DB::Relsegment->new() and Bio::DB::GFF->segment() as a replacement for...
CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC
FAST::Bio::Seq - Sequence object, with features
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 FAST::Bio...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
Bio::Das::Feature - A genomic annotation
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
Bio::ToolBox::Data - Reading, writing, and manipulating data structure
This module works with the primary Bio::ToolBox Data structure. Simply, it is a complex data structure representing a tabbed-delimited table (array of arrays), with plenty of options for metadata. Many common bioinformatic file formats are simply tab...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC
Bio::DB::GFF::Typename - The name of a feature type
Bio::DB::GFF::Typename objects encapsulate the combination of feature method and source used by the GFF flat file format. They can be used in the Bio::DB::GFF modules wherever a feature type is called for. Since there are relatively few types and man...
CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC
Bio::DB::Das::Chado - DAS-style access to a chado database
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