Search results for "dist:BioPerl Bio::SeqAnalysisParserI"
Bio::SeqAnalysisParserI - Sequence analysis output parser interface
SeqAnalysisParserI is a generic interface for describing sequence analysis result parsers. Sequence analysis in this sense is a search for similarities or the identification of features on the sequence, like a databank search or a a gene prediction r...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable of creating SeqAnalysisParserI compliant parsers
This is an interface for factory classes capable of instantiating SeqAnalysisParserI implementing parsers. The concept behind the interface is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. See Bio::SeqA...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser
This class provides a simple GFF parser and writer. In the sense of a SeqAnalysisParser, it parses an input file or stream into SeqFeatureI objects, but is not in any way specific to a particular analysis program and the output that program produces....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::MZEF - Results of one MZEF run
The MZEF module provides a parser for MZEF gene structure prediction output. This module inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Genscan - Results of one Genscan run
The Genscan module provides a parser for Genscan gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object. This module also implements the Bio::SeqAnalysisParserI interface, and thus can...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::ESTScan - Results of one ESTScan run
The ESTScan module provides a parser for ESTScan coding region prediction output. This module inherits off Bio::Tools::AnalysisResult and therefore implements the Bio::SeqAnalysisParserI interface. See Bio::SeqAnalysisParserI....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Fgenesh - parse results of one Fgenesh run
The Fgenesh module provides a parser for Fgenesh (version 2) gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object. This module also implements the Bio::SeqAnalysisParserI interface, ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Eponine - Results of one Eponine run
Parser for Eponine, a probabilistic transcription start site detector optimized for mammalian genomic sequence. This module inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI (see Bio::Tools::AnalysisResult and B...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions. It will create gene objects from the prediction report which can be attached to a sequence using Bioperl objects, or output as GFF suitable for loading into Bio::DB::GFF for u...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Genemark - Results of one Genemark run
The Genemark module provides a parser for Genemark gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object. This module has been developed around genemark.hmm for eukaryots v2.2a and wi...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AnalysisParserI - Generic analysis output parser interface
AnalysisParserI is a interface for describing generic analysis result parsers. This module makes no assumption about the nature of analysis being parsed, only that zero or more result sets can be obtained from the input source. This module was derive...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output
This script will parse tRNAscan-SE output. Just the tabular output of the tRNA locations in the genome for now....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Sim4::Results - Results of one Sim4 run
The sim4 module provides a parser and results object for sim4 output. The sim4 results are specialised types of SeqFeatures, meaning you can add them to AnnSeq objects fine, and manipulate them in the "normal" seqfeature manner. The sim4 Exon objects...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers
The AnalysisResult module is supposed to be the base class for modules encapsulating parsers and interpreters for the result of a analysis that was carried out with a query sequence. The notion of an analysis represented by this base class is that of...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Spidey::Results - Results of a Spidey run
The spidey module provides a parser and results object for spidey output. The spidey results are specialised types of SeqFeatures, meaning you can add them to AnnSeq objects fine, and manipulate them in the "normal" seqfeature manner. The spidey Exon...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI compliant parsers
This is a factory class capable of instantiating SeqAnalysisParserI implementing parsers. The concept behind this class and the interface it implements (Bio::Factory::SeqAnalysisParserFactoryI) is a generic analysis result parsing in high-throughput ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC