Search results for "Bio::SeqI"
Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guaranteed to get for any Bio::SeqI. For most users of the package the documentation (and methods) in this class are not at useful - this is a develo...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::DB::SeqI - Abstract Interface for Sequence databases
- Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq
- Bio::SeqFeatureI - Abstract interface of a Sequence Feature
- 57 more results from BioPerl »
FAST::Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
FAST::Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guarenteed to get for any FAST::Bio::SeqI - for most users of the package the documentation (and methods) in this class are not at useful - thi...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::DB::SeqI - Abstract Interface for Sequence databases
- FAST::Bio::MySeqI - Abstract Interface of Sequence (with features)
- FAST::Bio::GapSeqI - GapSeq interface, for gapped sequences
- 39 more results from FAST »
Bio::DB::SeqFeature::NormalizedFeatureI - Interface for normalized features
This is an extremely simple interface that contains a single method, subfeatures_are_normalized(). This method returns a true value. Bio::DB::SeqFeature::Store feature classes will inherit this interface to flag that they are able to store subfeature...
CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC - Search in distribution- Bio::DB::SeqFeature::NormalizedTableFeatureI - Interface for normalized features whose hierarchy is stored in a table
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::Glyph::cds - The "cds" glyph
- Bio::Graphics::Glyph::trace - A glyph that visualizes a trace file
- Bio::Graphics::Glyph::merged_alignment - The "merged_alignment" glyph
- 68 more results from Bio-Graphics »
SeqDiff - A tool to find the differences between two Seq objects.
The SeqDiff tool presented here will compare two Bio::Seq objects. It first looks through both objects and matches their features based on some criteria. It then recursively compares each pair of features and returns the comparison. Originally the pa...
BLUECURIO/SeqDiff-v0.1 - 12 Feb 2010 16:18:40 UTC - Search in distribution
load_seqdatabase.pl
This script loads a BioSQL database with sequences. There are a number of options that have to do with where the database is and how it's accessed and the format and namespace of the input files. These are followed by any number of file names. The fi...
CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 UTC - Search in distribution- Bio::DB::DBAdaptorI - DESCRIPTION of Interface
- Bio::DB::BioSQL::TermAdaptor - DESCRIPTION of Object
- Bio::DB::BioSQL::BasePersistenceAdaptor - DESCRIPTION of Object
- 9 more results from BioPerl-DB »
Bio::FeatureIO - Handler for FeatureIO
An I/O iterator subsystem for genomic sequence features. Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the format objects, which most people should...
CJFIELDS/Bio-FeatureIO-1.6.905 - 05 Sep 2014 17:34:58 UTC - Search in distribution
PerlIO::via::SeqIO - PerlIO layer for biological sequence formats
"PerlIO::via::SeqIO" attempts to provide an easy option for harnessing the magic sequence format I/O of the BioPerl (<http://bioperl.org>) toolkit. Opening a biological sequence file under "via(SeqIO)" yields a filehandle that can be used to read and...
MAJENSEN/PerlIO-via-SeqIO-0.0322 - 05 Dec 2009 20:28:53 UTC - Search in distribution
Bio::DB::GenBank - Database object interface to GenBank
Allows the dynamic retrieval of Bio::Seq sequence objects from the GenBank database at NCBI, via an Entrez query. WARNING: Please do NOT spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. Note that when quer...
CJFIELDS/Bio-DB-NCBIHelper-1.7.8 - 15 Dec 2023 04:25:18 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- Bio::DB::GFF::Segment - Simple DNA segment object
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::SoapEUtilities - Interface to the NCBI Entrez web service *BETA*
This module allows the user to query the NCBI Entrez database via its SOAP (Simple Object Access Protocol) web service (described at <http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.h tml>). The basic tools ("einfo, esearch, eli...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution- Bio::Tools::Run::Match - Wrapper for Transfac's match(TM)
- Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
- Bio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program
- 4 more results from BioPerl-Run »
Bio::Cluster::UniGene - UniGene object
This UniGene object implements the Bio::Cluster::UniGeneI interface for the representation if UniGene clusters in Bioperl. It is returned by the Bio::ClusterIO parser for unigene format and contains all the data associated with one UniGene record. Th...
CJFIELDS/Bio-Cluster-1.7.3 - 01 Oct 2018 04:35:53 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
lib/Bio/DB/SeqFeature/Store/Alias.pm
This module can be used as a wrapper around any BioPerl database that supports the get_feature_by_name() method. It allows you to dynamically override the type, source, method and display name of each feature, as well as to assign new metadata attrib...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC - Search in distribution- Bio::Graphics::Browser2::PadAlignment - Insert pads into a multiple alignment
Bio::Community::Member - The basic constituent of a biological community
A Bio::Community::Member represents an organism, individual, species, amplicon sequence, shotgun sequence or anything you like....
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC - Search in distribution- Bio::Community::Role::Sequenced - Role for objects that have a sequence
Bio::Tools::Primer3Redux::Result
This is a simple holder class for Primer3 sequence results. The sequence used by default is the one returned in the Primer3 results, but one can pass in a (more-SeqFeature/Annotation-rich) version as a Bio::Seq using attach_seq() (see below for more ...
CJFIELDS/Bio-Tools-Primer3Redux-0.09 - 11 Jun 2011 04:03:42 UTC - Search in distribution
Bio::Chado::Schema::Result::Sequence::Feature
A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cros...
RBUELS/Bio-Chado-Schema-0.20000 - 06 Jul 2012 19:06:31 UTC - Search in distribution