Search results for "Bio::Annotation::Reference"
Bio::Annotation::Reference - Specialised DBLink object for Literature References
Object which presents a literature reference. This is considered to be a specialised form of database link. The additional methods provided are all set/get methods to store strings commonly associated with references, in particular title, location (i...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::AnnotationI - Annotation interface
- Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
- bp_genbank2gff3.pl - Genbank-gtgbrowse-friendly GFF3
- 35 more results from BioPerl »
FAST::Bio::Annotation::Reference - Specialised DBLink object for Literature References
Object which presents a literature reference. This is considered to be a specialised form of database link. The additional methods provided are all set/get methods to store strings commonly associated with references, in particular title, location (i...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::AnnotationI - Annotation interface
- FAST::Bio::Seq - Sequence object, with features
- FAST::Bio::SeqIO::chadoxml - chadoxml sequence output stream
- 27 more results from FAST »
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::Segment - Simple DNA segment object
- Bio::DB::GFF::Adaptor::dbi::pg - Database adaptor for a specific postgres schema
- 3 more results from Bio-DB-GFF »
Bio::Biblio::Ref - representation of a bibliographic reference
A storage object for a general bibliographic reference (a citation). See its place in the class hierarchy in http://www.ebi.ac.uk/~senger/openbqs/images/bibobjects_perl.gif Attributes The following attributes are specific to this class, and they are ...
CDRAUG/Bio-Biblio-1.70 - 24 Mar 2013 00:19:52 UTC - Search in distribution
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
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
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
load_ontology.pl
This script loads a BioSQL database with an ontology. There are a number of options to do with where the BioSQL database is (ie, hostname, user for database, password, database name) followed by the database name you wish to load this into and then a...
CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 UTC - Search in distribution- load_seqdatabase.pl
- Bio::DB::Query::DBQueryResult - DESCRIPTION of Object
- Bio::DB::BioSQL::TermAdaptor - DESCRIPTION of Object
- 12 more results from BioPerl-DB »
get_features.pl - A program to collect and filter annotated features from source files.
This program will extract a list of features from a database or input annotation file and write them out to a file. Features may be selected using their feature type (the 3rd column in a GFF or GTF file). When selecting features from a database, type...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution- get_relative_data.pl - A program to collect data in bins around a relative position.
- get_intersecting_features.pl - A program to pull out overlapping features from the database.
- correlate_position_data.pl - A script to calculate correlations between two datasets along the length of a feature.
- 6 more results from Bio-ToolBox »
Bio::FdrFet - Perl extension for False Discovery Rate and Fisher Exact Test applied to pathway analysis.
Bio::FdrFet implements the False Discovery Rate Fisher Exact Test of gene expression analysis applied to pathways described in the paper by Ruiru Ji, Karl-Heinz Ott, Roumyana Yordanova, and Robert E Bruccoleri. A copy of the paper is included with th...
BRUC/Bio-FdrFet-0.05 - 03 Jan 2015 19:55:10 UTC - Search in distribution
gff2bed.pl - Convert (non-spliced) GFF3 to BED12
Convert feature annotation of non-spliced organisms in GFF3 format to BED12. A separate BED12 file will be created for each genomic feature type (eg CDS, tRNA, rRNA, ncRNA, etc.). This script serves as a reference implementation of code fragments fro...
MTW/Bio-ViennaNGS-v0.19.2 - 11 Dec 2018 13:25:00 UTC - Search in distribution- Bio::ViennaNGS - A Perl distribution for Next-Generation Sequencing (NGS) data analysis
Alvis::NLPPlatform - Perl extension for linguistically annotating XML documents in Alvis
This module is the main part of the Alvis NLP platform. It provides overall methods for the linguistic annotation of web documents. Linguistic annotations depend on the configuration variables and dependencies between linguistic steps. Input document...
THHAMON/Alvis-NLPPlatform-0.6 - 16 Apr 2008 17:19:55 UTC - Search in distribution
Alien::SeqAlignment::hmmer3 - find, build and install the hmmer3 tools
This distribution provides HMMER3 so that it can be used by other Perl distributions that are on CPAN. The source code will be downloaded from the HMMER3 website, if the HMMER3 is not found in the system path. The url used is : http://eddylab.org/sof...
CHRISARG/Alien-SeqAlignment-hmmer3-0.03 - 24 Mar 2024 03:13:58 UTC - Search in distribution
Bio::ASN1::EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene.
Bio::ASN1::EntrezGene is a regular expression-based Perl Parser for NCBI Entrez Gene genome databases (<http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene>). It parses an ASN.1-formatted Entrez Gene record and returns a data structure that contains al...
CJFIELDS/Bio-ASN1-EntrezGene-1.73 - 25 Sep 2018 02:32:11 UTC - Search in distribution- Bio::ASN1::Sequence - Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences.
- Bio::SeqIO::entrezgene - Entrez Gene ASN1 parser
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
CracTools::Utils - A set of useful functions
Bio::Lite is a set of subroutines that aims to answer similar questions as Bio-perl distribution in a FAST and SIMPLE way. Bio::Lite does not make use of complexe data struture, or objects, that would lead to a slow execution. All methods can be impo...
JAUDOUX/CracTools-1.251 - 09 Jun 2017 15:29:56 UTC - Search in distribution