Boulder::Genbank - Fetch Genbank data records as parsed Boulder Stones River stage zero No dependents

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 GMT - Search in distribution

Bio::DB::GenBank - Database object interface to GenBank River stage one • 1 direct dependent • 1 total dependent

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-1.7.4 - 11 Mar 2019 02:31:32 GMT - Search in distribution

Bio::SeqIO::genbank - GenBank sequence input/output stream River stage two • 71 direct dependents • 74 total dependents

This object can transform 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 _post...

CDRAUG/BioPerl-1.7.6 - 28 Aug 2019 11:42:06 GMT - Search in distribution

FAST::Bio::SeqIO::genbank - GenBank sequence input/output stream River stage zero No dependents

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 GMT - Search in distribution

genbank-parser.pl - parse GenBank records into YAML River stage zero No dependents

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 GMT - Search in distribution

pod::GENBANK_HOWTO River stage zero No dependents

LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 GMT - Search in distribution

bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files. River stage one • 1 direct dependent • 1 total dependent

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...

CDIESH/Bio-DB-GFF-1.7.3 - 19 Feb 2019 19:18:29 GMT - Search in distribution

bp_genbank_ref_extractor - Retrieves all related sequences for a list of searches on Entrez gene River stage zero No dependents

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-1.75 - 26 Sep 2016 04:08:04 GMT - Search in distribution

BS_AddFromGenbank.pl River stage zero No dependents

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 GMT - Search in distribution

cx-genbank2chaos.pl.pl River stage zero No dependents

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 GMT - Search in distribution

Bio::Das - Interface to Distributed Annotation System River stage zero No dependents

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 GMT - Search in distribution

Mecom - A Perl module for protein contact interfaces evolutive analysis River stage zero No dependents

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 GMT - Search in distribution

Bio::Graphics::Panel - Generate GD images of Bio::Seq objects River stage one • 3 direct dependents • 3 total dependents

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 GMT - Search in distribution

SeqDiff - A tool to find the differences between two Seq objects. River stage zero No dependents

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 GMT - Search in distribution

bioseq - Manipulation of FASTA sequences based on BioPerl River stage zero No dependents

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...

ROCKY/Bio-BPWrapper-1.12 - 15 Aug 2017 20:30:37 GMT - Search in distribution

load_seqdatabase.pl River stage zero No dependents

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 GMT - Search in distribution

FASTAParse - A light-weight parsing module for handling FASTA formatted sequence within larger perl applications. River stage zero No dependents

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 GMT - Search in distribution

GD_Juggle_Codons.pl River stage one • 1 direct dependent • 1 total dependent

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-5.54 - 04 Dec 2015 20:13:38 GMT - Search in distribution

Bio::Network::ProteinNet - a representation of a protein interaction graph. River stage zero No dependents

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 GMT - Search in distribution

Bio::Phylo - Phylogenetic analysis using perl River stage two • 8 direct dependents • 12 total dependents

This is the base class for the Bio::Phylo package for phylogenetic analysis using object-oriented perl5. In this file, methods are defined that are performed by other objects in the Bio::Phylo release that inherit from this base class (which you norm...

RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 GMT - Search in distribution

45 results (0.073 seconds)