Search results for "module:Bio::DB::GenBank"
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
Bio::DB::Query::GenBank - Build a GenBank Entrez Query
This class encapsulates NCBI Entrez queries. It can be used to store a list of GI numbers, to translate an Entrez query expression into a list of GI numbers, or to count the number of terms that would be returned by a query. Once created, the query o...
CJFIELDS/Bio-DB-NCBIHelper-1.7.8 - 15 Dec 2023 04:25:18 UTC
Bio::DB::Flat::BDB::genbank - genbank adaptor for Open-bio standard BDB-indexed flat file
This module allows genbank files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq - Sequence object, with features
A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently Bio::Prim...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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
Bio::Taxon - A node in a represented taxonomy
This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediate nodes not just the specie...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::EMBL - Database object interface for EMBL entry retrieval
Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL database using the dbfetch script at EBI: <http://www.ebi.ac.uk/Tools/dbfetch/dbfetch>. In order to make changes transparent we have host type (currently only ebi) and location (...
CJFIELDS/Bio-DB-EMBL-1.7.4 - 04 Mar 2019 05:02:40 UTC
Bio::DB::Qual - Fast indexed access to quality files
Bio::DB::Qual provides indexed access to a single Fasta file, several files, or a directory of files. It provides random access to each quality score entry without having to read the file from the beginning. Access to subqualities (portions of a qual...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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
Bio::DB::Flat - Interface for indexed flat files
This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see Bio::Index::Abstract), this is specialized to work with the "flat index" and BerkeleyDB indexed flat fil...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
FAST::Bio::Seq - Sequence object, with features
A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently FAST::Bio...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
Bio::DB::Fasta - Fast indexed access to fasta files
Bio::DB::Fasta provides indexed access to a single Fasta file, several files, or a directory of files. It provides persistent random access to each sequence entry (either as a Bio::PrimarySeqI-compliant object or a string), and to subsequences within...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::QueryI - Object Interface to queryable sequence databases
This interface provides facilities for managing sequence queries such as those offered by Entrez. A query object is created by calling new() with a database-specific argument list. From the query object you can either obtain the list of IDs returned ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::PrimarySeq - Bioperl lightweight sequence object
PrimarySeq is a lightweight sequence object, storing the sequence, its name, a computer-useful unique name, and other fundamental attributes. It does not contain sequence features or other information. To have a sequence with sequence features you sh...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::RefSeq - Database object interface for RefSeq retrieval
Allows the dynamic retrieval of sequence objects Bio::Seq from the RefSeq nucleotide database using the dbfetch script at EBI: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch At this time the module specifically retrieves nucleotide sequences only. In ord...
CJFIELDS/Bio-DB-RefSeq-1.7.4 - 07 Dec 2019 22:10:26 UTC
FAST::Bio::Taxon - A node in a represented taxonomy
This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called FAST::Bio::Species. This new implementation allows representation of the intermediate nodes not just the ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
Bio::DB::DBFetch - Database object for retrieving using the dbfetch script
Allows the dynamic retrieval of entries from databases using the dbfetch script at EBI: http://www.ebi.ac.uk/cgi-bin/dbfetch. In order to make changes transparent we have host type (currently only ebi) and location (defaults to ebi) separated out. Th...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeatureI - Abstract interface of a Sequence Feature
This interface is the functions one can expect for any Sequence Feature, whatever its implementation or whether it is a more complex type (eg, a Gene). This object does not actually provide any implementation, it just provides the definitions of what...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::GenPept - Database object interface to GenPept
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept 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. Batch Entrez supp...
CJFIELDS/Bio-DB-NCBIHelper-1.7.8 - 15 Dec 2023 04:25:18 UTC
Bio::DB::SwissProt - Database object interface to SwissProt retrieval
SwissProt is a curated database of proteins managed by the Swiss Bioinformatics Institute. Additional tools for parsing and manipulating swissprot files can be found at ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/. Allows the dynamic retrie...
CJFIELDS/Bio-DB-SwissProt-1.7.4 - 07 Dec 2019 22:09:00 UTC