Search results for "Bio::Annotation"
Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI object
Provides a Bio::AnnotationI object which contains a Bio::Tree::TreeI, which can be added to a Bio::AnnotationCollectionI, which in turn be attached to a Bio::AnnotatableI (typically a Bio::AlignI object)...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::Annotation::Target - Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
- Bio::Annotation::DBLink - untyped links between databases
- Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
- 71 more results from BioPerl »
FAST::Bio::Annotation::DBLink - untyped links between databases
Provides an object which represents a link from one object to something in another database without prescribing what is in the other database. Aside from FAST::Bio::AnnotationI, this class also implements FAST::Bio::IdentifiableI....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::Annotation::Target - Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
- FAST::Bio::Annotation::Comment - A comment object, holding text
- FAST::Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
- 51 more results from FAST »
Bio::AutomatedAnnotation - Automated annotation of assemblies
VOFFFORD/Bio-AutomatedAnnotation-1.182770
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04 Oct 2018 13:47:56 UTC
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- Bio::AutomatedAnnotation::Exceptions - Exceptions for input data
- Bio::AutomatedAnnotation::External::Cmscan - Run and parse the output of cmscan
- Bio::AutomatedAnnotation::GeneNamesFromGFF - Parse a GFF and efficiently extract out the Gene Names
- 10 more results from Bio-AutomatedAnnotation »
Bio::Roary::ParseGFFAnnotationRole - A role for parsing a gff file efficiently
AJPAGE/Bio-Roary-3.13.0
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06 Nov 2019 21:32:21 UTC
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- Bio::Roary::CommandLine::TransferAnnotationToGroups - Take in a groups file and a set of GFF files and transfer the consensus annotation
- transfer_annotation_to_groups - Take in a groups file and a set of GFF files and transfer the consensus annotation
Bio::KBase::GenomeAnnotation::Client
RDO/Bio-KBase-0.06
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15 Aug 2012 23:56:34 UTC
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Bio::DB::BioSQL::AnnotationCollectionAdaptor - DESCRIPTION of Object
Describe the object here...
CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 UTC - Search in distribution- Bio::DB::BioSQL::Pg::AnnotationCollectionAdaptorDriver - DESCRIPTION of Object
- Bio::DB::BioSQL::mysql::AnnotationCollectionAdaptorDriver - DESCRIPTION of Object
- Bio::DB::BioSQL::Oracle::AnnotationCollectionAdaptorDriver - DESCRIPTION of Object
- 15 more results from BioPerl-DB »
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 - Search in distribution- Bio::Das::Type - A sequence annotation type
- Bio::Das::Feature - A genomic annotation
- Bio::Das::Segment - Serial access to Bio::Das sequence "segments"
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 - Search in distribution- Bio::DB::GFF::Feature - A relative segment identified by a feature type
- Bio::DB::GFF::Adaptor::dbi::pg - Database adaptor for a specific postgres schema
- Bio::DB::GFF::Segment - Simple DNA segment object
- 3 more results from Bio-DB-GFF »
Perl6::Form - Implements the Perl 6 'form' built-in
Formats are Perl 5's mechanism for creating text templates with fixed-width fields. Those fields are then filled in using values from prespecified package variables. Unlike Perl 5, Perl 6 doesn't have a "format" keyword. Or the associated built-in fo...
DCONWAY/Perl6-Form-0.090 - 09 Jan 2019 00:23:27 UTC - Search in distribution
data2wig.pl - A program to convert a generic data file into a wig file.
This program will convert any tab-delimited data text file into a wiggle formatted text file. This requires that the file contains not only the scores bu also chromosomal coordinates, i.e. chromosome, start, and (optionally) stop. The program should ...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution- data2bed.pl - A program to convert a data file to a bed file.
- db_setup.pl - A program to setup a SeqFeature::Store SQLite database from UCSC data
- get_datasets.pl - A program to collect data for a list of features
- 16 more results from Bio-ToolBox »
wgs2ncbi - prepares whole genome sequencing projects for submission to NCBI
"wgs2ncbi" is a script that helps users prepare submissions of annotated, whole genomes to NCBI. It does this by performing a number of actions that need to be taken in sequence. Each of these actions need to be invoked as a subcommand (i.e. "wgs2ncb...
RVOSA/Bio-WGS2NCBI-v0.1.2 - 23 Jan 2020 15:54:29 UTC - Search in distribution- Bio::WGS2NCBI - module to assist in submitting whole genome sequencing projects to NCBI
- Bio::WGS2NCBI::Feature - base class for sequence features
pod::FAQ
LDS/GBrowse-2.56
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15 Jan 2017 21:29:11 UTC
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- pod::INSTALL
- process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
- pod::DAS_HOWTO
- 8 more results from GBrowse »
GO::AppHandle - Gene Ontology Data API handle
This is a module for accessing Gene Ontology data sources, e.g the GO relational database. It defines a set of methods that provide a consistent interface independent of the way the GO data is stored. For an explanation of the GO project, please visi...
SJCARBON/go-db-perl-0.04 - 21 Dec 2009 21:56:44 UTC - Search in distribution
Manual
LMEUNIER/Bio-Palantir-0.211420
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22 May 2021 20:37:07 UTC
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- Bio::Palantir - core classes and utilities for Bio::Palantir
- Bio::Palantir::Refiner - front-end class for Bio::Palantir::Refiner module, wich handles the refinement of NRPS/PKS BGC annotations
Bio::Glite - G-language Genome Analysis Environment REST service interface module
The G-language GAE fully supports most sequence databases. Stored annotation information: LOCUS $gb->{LOCUS}->{id} -accession number $gb->{LOCUS}->{length} -length of sequence $gb->{LOCUS}->{nucleotide} -type of sequence ex. DNA, RNA $gb->{LOCUS}->{c...
GAOU/Bio-Glite-0.10 - 30 Mar 2009 14:38:31 UTC - Search in distribution
bp_genbank_ref_extractor - Retrieves all related sequences for a list of searches on Entrez gene
This script searches on *Entrez Gene* database and retrieves not only the gene sequence but also the related transcript and protein sequences. The gene UIDs of multiple searches are collected before attempting to retrieve them so each gene will only ...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC - Search in distribution
format-tree.pl - Format (and annotate) trees for printing
DBAURAIN/Bio-MUST-Core-0.240390
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08 Feb 2024 21:02:36 UTC
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Bio::NEXUS
This User Manual explains the motivation for developing the Bio::NEXUS library, the principles underlying its organization, and its use in developing software for evolutionary informatics. This manual also provides information on how to use two demon...
ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 UTC - Search in distribution
Data::Type::RFC - request for comments on the design of Data::Type
This is the API documentation. Every candidate datatype must be sustain the following conventions before it should be released. Comments are requested....
MUENALAN/Data-Type-0.02.02 - 31 Dec 2009 13:48:47 UTC - Search in distribution