Search results for "genbank"
Boulder::Genbank - Fetch Genbank data records as parsed Boulder Stones
Boulder::Genbank provides retrieval and parsing services for NCBI Genbank-format records. It returns Genbank entries in Stone format, allowing easy access to the various fields and values. Boulder::Genbank is a descendent of Boulder::Stream, and prov...
LDS/Boulder-1.30 - 14 Dec 2002 02:06:29 UTC - Search in distribution- Stone - In-memory storage for hierarchical tag/value data structures
- Boulder::Blast - Parse and read BLAST files
- Boulder - An API for hierarchical tag/value structures
- 10 more results from Boulder »
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::Query::GenBank - Build a GenBank Entrez Query
- bp_download_query_genbank - script to query Genbank and retrieve records
- Bio::DB::GenPept - Database object interface to GenPept
- 2 more results from Bio-DB-NCBIHelper »
Bio::Index::GenBank - Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
By default the index that is created uses the LOCUS, ACCESSION, and VERSION identifiers as keys. Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic functionality for indexing GenBank files, and retrieving t...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::SeqIO::genbank - GenBank sequence input/output stream
- Bio::DB::Flat::BDB::genbank - genbank adaptor for Open-bio standard BDB-indexed flat file
- bp_genbank2gff3.pl - Genbank-gtgbrowse-friendly GFF3
- 59 more results from BioPerl »
FAST::Bio::SeqIO::genbank - GenBank sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from GenBank flat file databases. There is some flexibility here about how to write GenBank output that is not fully documented. Optional functions _show_dna() (output only) shows the dna or not...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- fastr - character-based transformations on sequence records
- fascut - select biosequence record data by character or field ranges
- FAST - FAST Analysis of Sequences Toolbox
- 45 more results from FAST »
genbank-parser.pl - parse GenBank records into YAML
This is little more than an example showing a trivial use of Bio::GenBankParser. Here we convert a stream of files into YAML on STDOUT....
KCLARK/Bio-GenBankParser-0.05 - 23 Jun 2010 17:00:02 UTC - Search in distribution- Bio::GenBankParser - Parse::RecDescent parser for a GenBank record
pod::GENBANK_HOWTO
LDS/GBrowse-2.56
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15 Jan 2017 21:29:11 UTC
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Search in distribution
- load_genbank.pl - Load a Bio::DB::GFF database from GENBANK files.
- pod::INSTALL
- pod::CONFIGURE_HOWTO
- 1 more result from GBrowse »
bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files.
This script loads a Bio::DB::GFF database with the features contained in a either a local genbank file or an accession that is fetched from genbank. Various command-line options allow you to control which database to load and whether to allow an exis...
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::DB::GFF::Adaptor::biofetch - Cache BioFetch objects in a Bio::DB::GFF database
- Bio::DB::GFF::Adaptor::biofetch_oracle - Cache BioFetch objects in a Bio::DB::GFF database
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
BS_AddFromGenbank.pl
This utility adds chromosome files to the BioStudio genome repository from genbank inputs. Because BioStudio requires that every feature have a unique ID, this utility will also check to make sure that even subfeatures can be uniquely identified, and...
NOTDOCTOR/Bio-BioStudio-2.11 - 04 Dec 2015 18:59:24 UTC - Search in distribution
cx-genbank2chaos.pl.pl
Converts a genbank file to a chaos xml file (or a collection of chaos xml files). The genbank file is 'unflattened' in order to infer the relationships between features with the -islands option set, this loops through a list of genbank-formatted file...
CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC - Search in distribution- cx-genbank2chaos.pl.pl
- Bio::Chaos - utility class for handling Chaos-XML
- Bio::Chaos::ChaosGraph - object for representing a chaos-xml dataset
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
Mecom - A Perl module for protein contact interfaces evolutive analysis
This module integrates a workflow aimed to address the evolvability of the contact interfaces within a protein complex. The method "Mecom->run" launchs the whole analysis. Also, such workflow is divided into the following steps: Step 1, Structural an...
HVALVERDE/Mecom-1.15 - 13 Jul 2013 18:55:01 UTC - Search in distribution
Bio::Graphics::Panel - Generate GD images of Bio::Seq objects
The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature and Das::Segment::Feature objects. It can be used to draw sequence annotations, ph...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC - Search in distribution- Bio::Graphics::FeatureFile - A set of Bio::Graphics features, stored in a file
- Bio::Graphics - Generate GD images of Bio::Seq objects
- Bio::Graphics::Feature - A simple feature object for use with Bio::Graphics::Panel
dkbench - DKbench Perl Benchmark launch script
This is the benchmarking script, part of the Benchmark::DKbench distribution. See POD on the main module for info: perldoc Benchmark::DKbench...
DKECHAG/Benchmark-DKbench-2.4 - 29 Sep 2023 23:09:15 UTC - Search in distribution- setup_dkbench - DKbench Perl CPU Benchmark utility setup script
- Benchmark::DKbench - Perl CPU Benchmark
bioseq - Manipulation of FASTA sequences based on BioPerl
bioseq is a command-line utility for common, routine sequence manipulations based on BioPerl modules including Bio::Seq, Bio::SeqIO, Bio::SeqUtils, and Bio::Tools::SeqStats. By default, bioseq assumes that both the input and the output files are in F...
YZHERNAND/Bio-BPWrapper-1.15 - 27 Feb 2024 16:55:31 UTC - Search in distribution
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
FASTAParse - A light-weight parsing module for handling FASTA formatted sequence within larger perl applications.
FASTAParse is pretty simple in that it does one of two things: 1) loads a FASTA object from a chunk of text; 2) formats a FASTA object given explicit user input. See SYNOPSIS for example code for both functions. Once populated, individual sections of...
TWYLIE/FASTAParse-0.0.3 - 05 Apr 2008 03:28:25 UTC - Search in distribution
GD_Juggle_Codons.pl
Given at least one protein-coding gene as input, the Juggle_Codons script can use several algorithms to modify the sequence without altering its translation. It is thus possible to generate a sequence that is optimized for expression, as different as...
NOTDOCTOR/Bio-GeneDesign-5.56 - 19 Jun 2020 16:50:54 UTC - Search in distribution