Search results for "module:Bio::Emboss"
Bio::Emboss - Write EMBOSS programs in Perl
This module allows Perl programmers to access functions of the EMBOSS (European Molecular Biology Open Software Suite) package....
PERNST/Bio-Emboss-5.0.0.1 - 06 Sep 2007 16:28:46 UTC
Bio::Factory::EMBOSS - EMBOSS application factory class
The EMBOSS factory class encapsulates access to EMBOSS programs. A factory object allows creation of only known applications. If you want to check command line options before sending them to the program set $prog->verbose to positive integer. The val...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)
This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
FAST::Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)
This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output
This is a parser for the EMBOSS tool 'palindrome'. It will produce a Bio::Seq object for each sequence analyzed. The sequence will be empty (but will be of the correct length) and will have attached to it Bio::SeqFeature::FeaturePair objects which wi...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications
The EMBOSSApplication class can represent any EMBOSS program. It is created by a Bio::Factory::EMBOSS object. If you want to check command line options before sending them to the program set $prog->verbose to positive integer. The ADC description of ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Grep - Perl extension for searching in DNA and Protein sequences
Bio-Grep is a collection of Perl modules for searching in DNA and Protein sequences. It supports different back-ends, most importantly some (enhanced) suffix array implementations. Currently, there is no suffix array tool that works in all scenarios ...
LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC
Bio::AlignIO - Handler for AlignIO Formats
Bio::AlignIO is a handler module for the formats in the AlignIO set, for example, Bio::AlignIO::fasta. It is the officially sanctioned way of getting at the alignment objects. The resulting alignment is a Bio::Align::AlignI-compliant object. The idea...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::MCPrimers
Creates molecular cloning PCR primer pairs for a given gene so that the gene can be directionally inserted into a vector. Solver is generic, restriction enzymes and their order in the vector are specified in the caller....
SLENK/Bio-MCPrimers-2.5 - 13 Sep 2006 16:47:00 UTC
Bio::AnalysisI - An interface to any (local or remote) analysis tool
This interface contains all public methods for accessing and controlling local and remote analysis tools. It is meant to be used on the client side....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DOOP::DOOP - DOOP API main module
DoOP is a database containing orthologous clusters of promoters from Homo sapiens, Arabidopsis thaliana and other organisms. Visit the doop.abc.hu or doopsearch.abc.hu sites for more information or read the following article. Endre Barta, Endre Sebes...
RAZZOR/Bio-DOOP-DOOP-1.04 - 17 Aug 2009 12:59:38 UTC
FAST::Bio::AlignIO - Handler for AlignIO Formats
FAST::Bio::AlignIO is a handler module for the formats in the AlignIO set, for example, FAST::Bio::AlignIO::fasta. It is the officially sanctioned way of getting at the alignment objects. The resulting alignment is a FAST::Bio::Align::AlignI-complian...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers
The EMBOSSacd represents all the possible command line arguments that can be given to an EMBOSS application. Do not create this object directly. It will be created and attached to its corresponding Bio::Tools::Run::EMBOSSApplication if you set $appli...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Sigcleave - Bioperl object for sigcleave analysis
"Sigcleave" was a program distributed as part of the free EGCG add-on to earlier versions of the GCG Sequence Analysis package. A new implementation of the algorithm is now part of EMBOSS package. From the EGCG documentation: SigCleave uses the von H...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Prospect::Align - Package for overlaying multiple Prospect alignments
Bio::Prospect::Align represents an alignment of one or more Prospect structural alignments....
REECE/Bio-Prospect-1.04 - 19 Nov 2003 06:34:27 UTC
Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
This module is a parser for "est2genome" [EMBOSS] alignments of est/cdna sequence to genomic DNA. This is generally accepted as the best program for predicting splice sites based on est/dnas (as far as I know). This module currently does not try pull...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Run::Analysis - Module representing any (remote or local) analysis tool
The module represents an access to the local and/or remote analysis tools in a unified way that allows adding new access methods (protocols) seamlessly. At the moment of writing, there is available a *SOAP* access to almost all EMBOSS applications, r...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Grep::SearchSettings - Data structure for all search settings
Bio::Grep::SearchSettings is the data structure for all search settings. Not all back-ends will support every option....
LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC