Search results for "dist:BioPerl Bio::Emboss"
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
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::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::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
bp_fetch.pl - fetches sequences from bioperl indexed databases
Fetches sequences using the DB access systems in Bioperl. The most common use of this is to bp_fetch sequences from bioperl indices built using bpindex.pl, or to fetch sequences from the NCBI website The format for retrieving sequences is delibrately...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 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::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::Tools::pICalculator - calculate the isoelectric point of a protein
Calculates the isoelectric point of a protein, the pH at which there is no overall charge on the protein. Calculates the charge on a protein at a given pH. Can use built-in sets of pK values or custom pK sets....
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::Align::DNAStatistics - Calculate some statistics for a DNA alignment
This object contains routines for calculating various statistics and distances for DNA alignments. The routines are not well tested and do contain errors at this point. Work is underway to correct them, but do not expect this code to give you the rig...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Run::AnalysisFactory - A directory of analysis tools
The module represents a list of available analysis tools from a given location using a given access method. Additionally, for any of the available analyses, it can create an object of type "Bio::Tools::Run::Analysis". The module is a higher-level abs...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC