Search results for "Bio::SeqFeature::Generic"
Bio::SeqFeature::Generic - Generic SeqFeature
Bio::SeqFeature::Generic is a generic implementation for the 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 example, this is f...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::SeqFeature::Primer - Primer Generic SeqFeature
- Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
- Bio::Species - Generic species object.
- 35 more results from BioPerl »
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::Seq - Sequence object, with features
- FAST::Bio::Species - Generic species object.
- FAST::Bio::SeqIO::bsml - BSML sequence input/output stream
- 14 more results from FAST »
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::Store::Loader - Loader
- Bio::DB::SeqFeature::Store::berkeleydb - Storage and retrieval of sequence annotation data in Berkeleydb files
- 8 more results from Bio-DB-SeqFeature »
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 - Search in distribution- Bio::Graphics::Panel - Generate GD images of Bio::Seq objects
- Bio::Graphics::Glyph::trace - A glyph that visualizes a trace file
- Bio::Graphics::Glyph::segments - The "segments" glyph
- 9 more results from Bio-Graphics »
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
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.
- Bio::ToolBox - Tools for querying and analysis of genomic data
- Bio::ToolBox::Data - Reading, writing, and manipulating data structure
- 4 more results from Bio-ToolBox »
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::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
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
pod::CONFIGURE_HOWTO
LDS/GBrowse-2.56
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15 Jan 2017 21:29:11 UTC
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- Bio::Graphics::Browser::Plugin - Base class for gbrowse plugins.
- Bio::Graphics::Browser2::Plugin - Base class for gbrowse plugins.
- Bio::Graphics::Browser2::GFFhelper - Helps gbrowse plugins handle GFF
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::MAGE::BioSequence - Container module for classes in the MAGE package: BioSequence
This is a *package* module that encapsulates a number of classes in the Bio::MAGE hierarchy. These classes belong to the BioSequence package of the MAGE-OM object model....
JASONS/Bio-MAGE-20030502.3 - 14 May 2007 10:56:09 UTC - Search in distribution- Bio::MAGE::Describable - Class for the MAGE-OM API
- Bio::MAGE::BioSequence::BioSequence - Class for the MAGE-OM API
- Bio::MAGE::DesignElement::ReporterPosition - Class for the MAGE-OM API
- 4 more results from Bio-MAGE »
lib/Bio/DB/BigWig.pm
This module provides a high-level interface to Jim Kent's BigWig files, a type of indexed genome feature database that can be randomly accessed across the network. Please see http://genome.ucsc.edu/FAQ/FAQformat.html for information about creating th...
LDS/Bio-BigFile-1.07 - 24 Feb 2012 17:20:46 UTC - Search in distribution
Bio::Draw::FeatureStack - BioPerl module to generate GD images of stacked gene models
FeatureStack creates GD images of vertically stacked gene models to facilitate visual comparison of gene structures. Compared genes can be clusters of orthologous genes, gene family members, or any other genes of interest. FeatureStack takes an array...
CHRISFR/Bio-Draw-FeatureStack-0.03 - 29 Jun 2012 21:09:13 UTC - Search in distribution
Bio::Variation::VariantI - Sequence Change SeqFeature abstract class
This superclass defines common methods to basic sequence changes. The instantiable classes Bio::Variation::DNAMutation, Bio::Variation::RNAChange and Bio::Variation::AAChange use them. See Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and B...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC - Search in distribution
Bio::Tools::Hmmpfam - Parser for Hmmpfam program
Parser for Hmmpfam program. See also Bio::SearchIO::hmmer....
CJFIELDS/Bio-SearchIO-hmmer-1.7.3 - 25 Sep 2018 00:26:52 UTC - Search in distribution
Bio::Tools::Run::Coil - wrapper for ncoils program
This module is a wrapper for the ncoils program available via <http://www.russell.embl-heidelberg.de/coils/coils.tar.gz> for predicting coiled coils in protein sequences. By default it looks for an executable called *ncoils* and data/parameter files ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution- Bio::Tools::Run::Seg - Object for identifying low complexity regions in a given protein seequence.
- Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes in a given protein seequence.
- Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
- 7 more results from BioPerl-Run »
Bio::DB::Persistent::PersistentObject - makes a given object persistent
This class takes any Bioperl object for which an adaptor exists for a certain datastore and makes it implement Bio::DB::PersistentObjectI. There is one single caveat though. The wrapped object must not use any of the method names defined in Bio::DB::...
CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 UTC - Search in distribution
Bio::DB::Das::Chado::Segment::Feature
Not yet written...
SCAIN/Bio-DB-Das-Chado-0.35a - 07 Apr 2015 23:02:17 UTC - Search in distribution
Bio::Tools::Primer3Redux::Primer
This class is a simple subclass of Bio::SeqFeature::Generic that adds convenience accessor methods for primer-specific data, such as Tm, GC content, and other interesting bits of information returned from Primer3. Beyond that, the data can be persist...
CJFIELDS/Bio-Tools-Primer3Redux-0.09 - 11 Jun 2011 04:03:42 UTC - Search in distribution