Search results for "Bio::SeqFeature"
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 - Search in distribution- Bio::DB::SeqFeature::Store - Storage and retrieval of sequence annotation data
- Bio::DB::SeqFeature::Segment - Location-based access to genome annotation data
- Bio::DB::SeqFeature::NormalizedFeature - Normalized feature for use with Bio::DB::SeqFeature::Store
- 16 more results from Bio-DB-SeqFeature »
Bio::SeqFeature::Lite - Lightweight Bio::SeqFeatureI class
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::SeqFeature::SubSeq - Feature representing a subsequence
- Bio::SeqFeature::Primer - Primer Generic SeqFeature
- Bio::SeqFeature::Generic - Generic SeqFeature
- 94 more results from BioPerl »
Bio::ToolBox::SeqFeature - Fast, simple SeqFeature implementation
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-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution- data2wig.pl - A program to convert a generic data file into a wig file.
- data2bed.pl - A program to convert a data file to a bed file.
- get_features.pl - A program to collect and filter annotated features from source files.
- 23 more results from Bio-ToolBox »
Bio::SeqFeature::Annotated - PLEASE PUT SOMETHING HERE
None yet, complain to authors....
CJFIELDS/Bio-FeatureIO-1.6.905 - 05 Sep 2014 17:34:58 UTC - Search in distribution- Bio::FeatureIO - Handler for FeatureIO
- Bio::FeatureIO::bed - read/write features from UCSC BED format
- Bio::FeatureIO::gff - read/write GFF feature files
FAST::Bio::SeqFeature::Generic - Generic SeqFeature
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- FAST::Bio::SeqFeature::Similarity - A sequence feature based on similarity
- FAST::Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits
- FAST::Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity of two sequences.
- 44 more results from FAST »
Bio::BioStudio::SeqFeature::Tag - a feature representing a PCRTag
BioStudio functions...
NOTDOCTOR/Bio-BioStudio-2.11 - 04 Dec 2015 18:59:24 UTC - Search in distribution- Bio::BioStudio::SeqFeature::Chunk
- Bio::BioStudio::SeqFeature::Codon - a feature representing a codon
- Bio::BioStudio::SeqFeature::Custom
- 12 more results from Bio-BioStudio »
Bio::DB::Persistent::SeqFeature - Proxy object for database SeqFeatureI representations
No description yet ......
CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 UTC - Search in distribution- Bio::DB::BioSQL::SeqFeatureAdaptor - DESCRIPTION of Object
- Bio::DB::Persistent::PersistentObject - makes a given object persistent
Bio::MAGE::BioSequence::SeqFeature - Class for the MAGE-OM API
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::MAGE::BioSequence::SeqFeatureLocation - Class for the MAGE-OM API
- Bio::MAGE::BioSequence - Container module for classes in the MAGE package: BioSequence
- Bio::MAGE::Describable - Class for the MAGE-OM API
- 4 more results from Bio-MAGE »
Bio::DB::SeqFeature::Store::LoadHelper - Internal utility for Bio::DB::SeqFeature::Store
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
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
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
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 - Search in distribution
lib/Bio/Emboss/Methods.pm
PERNST/Bio-Emboss-5.0.0.1
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06 Sep 2007 16:28:46 UTC
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PrimerMap - generates a primer sequence graphical map
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
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- show-align2clustalw.pl - convert mummer alignment files to clustalw format
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 - Search in distribution
cx-genbank2chaos.pl.pl
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- cx-genbank2chaos.pl.pl
- Bio::Chaos::ChaosGraph - object for representing a chaos-xml dataset
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 - Search in distribution
Bio::Network::ProteinNet - a representation of a protein interaction graph.
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
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 - Search in distribution