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Author image David H. Ardell

Documentation

filter sites in alignments based on variation and gap-content
counts codon usage
analysis of monomer frequencies
Convert sequences or alignments to or from fasta format.
select biosequence record data by character or field ranges
Select sequences by numerical values of name,value pairs
print sequence records matching a pattern
print first sequence records on input
annotate sequence lengths to descriptions
concatenate sequence record data
reverse complement nucleotide sequences and alignments
sort sequences based on identifiers
regex-based substitutions on sequence records
print last sequence records on input
select sequence records by NCBI taxonomic names or IDs
sort sequence records based on NCBI taxonomy
character-based transformations on sequence records
Remove duplicate sequence records in a multifasta file or datastream.
tally sequences and sequence characters
translate sequences by a genetic code.
cut sites from alignments by regex-matching on features in an annotated GenBank file
search features from GenBank files and print corresponding sequences

Modules

FAST Analysis of Sequences Toolbox
An interface for describing sequence alignments.
Handler for AlignIO Formats
FAST::Bio::HandlerI-based generic data handler class for alignment-based data
ARP MSA Sequence input/output stream
bl2seq sequence input/output stream
clustalw sequence input/output stream
Parse EMBOSS alignment output (from applications water and needle)
fasta MSA Sequence input/output stream
Largemultifasta MSA Sequence input/output stream
Multiple Alignment Format sequence input stream
mase sequence input/output stream
Parse and Create MEGA format data files
meme sequence input/output stream
Metafasta MSA Sequence input/output stream
msf sequence input/output stream
NeXML format sequence alignment input/output stream driver
NEXUS format sequence input/output stream
pfam sequence input/output stream
PHYLIP format sequence input/output stream
po MSA Sequence input/output stream
proda sequence input/output stream
prodom sequence input/output stream
Read/Write PSI-BLAST profile alignment files
selex sequence input/output stream
stockholm sequence input/output stream
XMFA MSA Sequence input/output stream
Generic analysis output parser interface
Interface for analysis result objects
the base interface an annotatable object must implement
Instantiates a new FAST::Bio::AnnotationI (or derived class) through a factory
Default Perl implementation of AnnotationCollectionI
A comment object, holding text
untyped links between databases
An ontology term adapted to AnnotationI
Specialised DBLink object for Literature References
AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
Manages types for annotation collections
Interface for annotation collections
Annotation interface
Family Interface
Sequence Family object
Cluster Interface
Abstract interface for a sequence database
Abstract interface for a sequence database
Abstract Interface for Sequence databases
Access to a taxonomy database
Taxonomy Entrez driver
An implementation of FAST::Bio::DB::Taxonomy which uses local flat files
An implementation of FAST::Bio::DB::Taxonomy that accepts lists of words to build a database
interface for objects with human readable names and descriptions
This interface describes the basic event generator class.
An Event Handler Interface
A FeatureTable Location Parser
A factory interface for generating locations from a string
Interface for an object builder
Instantiates a new FAST::Bio::Root::RootI (or derived class) through a factory
A General object creator factory
This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
Interface describing the basics of a Sequence Stream.
the base interface an object with features must implement
GapSeq interface, for gapped sequences
Interface class for handler methods which interact with any event-driven parsers (drivers).
interface for objects with identifiers
A FAST::Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
Implementation of a Atomic Location on a Sequence
Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
Implementation of a Location on a Sequence which has unclear start and/or end locations
Abstract interface of a Location on a Sequence which has unclear start/end location
class implementing FAST::Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
Implementation of a Simple Location on a Sequence
Implementation of a Location on a Sequence which has multiple locations (start/end points)
Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
class implementing FAST::Bio::Location::CoordinatePolicy as the widest possible and reasonable range
Abstract interface of a Location on a Sequence
Interface definition for a FAST::Bio::PrimarySeq
Abstract Interface of Sequence (with features)
Keep track of where to find ontologies. Allows lookups by name.
An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
standard implementation of an Ontology
Interface a minimal Ontology implementation should satisfy
Interface for an ontology implementation
A repository of ontologies
a relationship for an ontology
Instantiates a new FAST::Bio::Ontology::RelationshipI (or derived class) through a factory
Interface for a relationship between ontology terms
a relationship type for an ontology
Graph adaptor for FAST::Bio::Ontology::SimpleGOEngine
Graph adaptor (v02.x) for FAST::Bio::Ontology::SimpleGOEngine
Implementation of OntologyEngineI interface
implementation of the interface for ontology terms
Instantiates a new FAST::Bio::Ontology::TermI (or derived class) through a factory
interface for ontology terms
Parser factory for Ontology formats
XML handler class for InterProParser
parse an InterPro XML file and persist the resulting terms to a Biosql database
Parser for InterPro xml files.
a base class parser for GO flat-file type formats
a parser for the Gene Ontology flat-file format
a parser for OBO flat-file format from Gene Ontology Consortium
a base class parser for simple hierarchy-by-indentation type formats
a parser for the Sequence Ontology flat-file format
Bioperl lightweight Sequence Object
Interface definition for a FAST::Bio::PrimarySeq
A base module for fast 'pull' parsing
Pure perl RangeI implementation
Range interface
module for fallback HTTP get operations when LWP:: is unavailable
Utility functions for FAST::Bio::Search:: BLAST objects
An object for statistics
A parser and HSP object for BlastN hsps
A "Generic" implementation of a High Scoring Pair
A factory to create FAST::Bio::Search::HSP::HSPI objects
Interface for a High Scoring Pair in a similarity search result
A parser and HSP object for hmmpfam hsps
FAST::Bio::Search::HSP::HSPI interface for pull parsers.
A parser and hit object for BLASTN hits
A generic implementation of the FAST::Bio::Search::Hit::HitI interface
A factory to create FAST::Bio::Search::Hit::HitI objects
Interface for a hit in a similarity search result
A parser and hit object for hmmpfam hits
FAST::Bio::Search::Hit::HitI interface for pull parsers.
A parser and result object for BLASTN results
CrossMatch-specific subclass of FAST::Bio::Search::Result::GenericResult
Generic Implementation of FAST::Bio::Search::Result::ResultI interface applicable to most search results.
A parser and result object for hmmpfam results
FAST::Bio::Search::Result::ResultI interface for 'pull' parsers
A factory to create FAST::Bio::Search::Result::ResultI objects
Abstract interface to Search Result objects
Utility functions for FAST::Bio::Search:: objects
A Base object for statistics
Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
An abstract Event Handler for Search Result parsing
Event Handler for SearchIO events.
Event Handler for SearchIO events.
Event Handler for SearchIO events.
Interface for outputting parsed Search results
Interface for outputting parsed search results in Gbrowse GFF format
Tab-delimited data for FAST::Bio::Search::HSP::HSPI objects
write a FAST::Bio::Search::ResultI in HTML
Tab-delimited data for FAST::Bio::Search::Hit::HitI objects
Outputs tab-delimited data for each FAST::Bio::Search::Result::ResultI object.
Object to implement writing a FAST::Bio::Search::ResultI in Text.
XML Handler for NCBI Blast XML parsing.
XML Handler for NCBI Blast PSIBLAST XML parsing.
a parser for axt format reports
Event generator for event based parsing of blast reports
A parser for BLAST output
Driver module for SearchIO for parsing NCBI -m 8/9 format
A SearchIO implementation of NCBI Blast XML parsing.
CrossMatch-specific subclass of FAST::Bio::SearchIO
SearchIO-based ERPIN parser
parser for Exonerate
A SearchIO parser for FASTA results
Event generator for parsing gmap reports (Z format)
A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
A parser for HMMER output (hmmpfam, hmmsearch)
DESCRIPTION of Object
A parser for HMMER output
SearchIO-based Infernal parser
a driver module for FAST::Bio::SearchIO to parse megablast reports (format 0)
A parser for PSL output (UCSC)
SearchIO-based RNAMotif parser
parser for Sim4 alignments
SearchIO parser for Jim Kent WABA program alignment output
Parsing of wise output as alignments
Sequence object, with features
LocatableSeq object that stores sequence as files in the tempdir
PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in FAST::Bio::Root::Root
Interface class for sequences that cache their residues in a temporary file
Generic superclass for sequence objects with residue-based meta information
array-based generic implementation of a sequence class with residue-based meta information
Interface for sequence objects with residue-based meta information
Bioperl lightweight Quality Object
Interface definition for a FAST::Bio::Seq::Qual
Implementation of sequence with residue quality and trace values
Module implementing a sequence created from a rich sequence database entry
interface for sequences from rich data sources, mostly databases
Configurable object builder for sequence stream parsers
Instantiates a new FAST::Bio::PrimarySeqI (or derived class) through a factory
Instantiates a new FAST::Bio::PrimarySeqI (or derived class) through a factory
Bioperl object packaging a sequence with its trace
Interface definition for a FAST::Bio::Seq::Trace
Sequence analysis output parser interface
hold pair feature information e.g. blast hits
a feature representing an exon
Interface for a feature representing an exon
A feature representing an arbitrarily complex structure of a gene
A feature representing an arbitrarily complex structure of a gene
superclass for non-coding features
A feature representing a transcript
Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
A feature representing an untranslated region that is part of a transcriptional unit
Generic SeqFeature
A sequence feature based on similarity
Sequence feature based on the similarity of two sequences.
generates unique persistent names for features
maps $seq_feature-gtprimary_tag
maps $seq_feature-gtprimary_tag
turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
Abstract interface of a Sequence Feature
[Developers] Abstract Interface of Sequence (with features)
Handler for SeqIO Formats
Helper class for Embl/Genbank feature tables
FAST::Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
Treating a set of files as a single input stream
abi trace sequence input/output stream
ace sequence input/output stream
AGAVE sequence output stream.
alf trace sequence input/output stream
asciitree sequence input/output stream
BSML sequence input/output stream
BSML sequence input/output stream using SAX
chadoxml sequence output stream
chaos sequence input/output stream
chaosxml sequence input/output stream
ctf trace sequence input/output stream
EMBL sequence input/output stream
EMBL sequence input/output stream
Entrez Gene ASN1 parser
sequence input/output stream from a MSExcel-formatted table
exp trace sequence input/output stream
fasta sequence input/output stream
fastq sequence input/output stream
FlyBase variant of chadoxml with sequence output stream
a class for parsing and writing game-XML
a class for handling feature elements
PerlSAX handler for game-XML
a base class for game-XML parsing
a class for writing game-XML
a class for handling game-XML sequences
GenBank handler-based push parser
GenBank sequence input/output stream using SAX
GCG sequence input/output stream
GenBank sequence input/output stream
InterProScan XML input/output stream
KEGG sequence input/output stream
method i/o on very large fasta sequence files
Lasergene sequence file input/output stream
LocusLink input/output stream
input stream for output by Teshima et al.'s mbs.
metafasta sequence input/output stream
input stream for output by Hudson's ms
NeXML sequence input/output stream
phd file input/output stream
PIR sequence input/output stream
pln trace sequence input/output stream
.qual file input/output stream
raw sequence file input/output stream
.scf file input/output stream
SeqXML sequence input/output stream
DNA strider sequence input/output stream
Swissprot sequence input/output stream
SwissProt/UniProt handler-based push parser
nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
sequence input/output stream from a delimited table
TIGR XML sequence input/output stream
Parse TIGR (new) XML
reading/writing sequences in NCBI TinySeq format
XML event handlers to support NCBI TinySeq XML parsing
ztr trace sequence input/output stream
Additional methods for PrimarySeq objects
Multiple alignments held as a set of sequences
Generic species object.
A node in a represented taxonomy
Base class for analysis result objects and parsers
Codon table object
A FAST::Bio::SeqAnalysisParserI compliant GFF format parser
Results of one Genewise run
Results of one Genomewise run
Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
Generates unique Seq objects from an ambiguous Seq object
Object holding statistics for one particular sequence
An object for the parameters used to run programs
A Base object for the parameters used to run programs
represent a sequence pattern or motif
Object holding statistics for one particular sequence
A Simple Tree Node
Interface describing a Tree Node
An Implementation of TreeI interface.
Decorated Interface implementing basic Tree exploration methods
A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
Bioperl alignment object
A base class for Web (any protocol) access
provides functions for generating lists
performance tips for using FAST::List::Gen
how to get the most out of FAST::List::Gen
the haskell prelude in perl5
perl6 / haskell like laziness in perl5
perl builtin functions with partial + lazy application
perl ops with partial + lazy application
perl6 meta operators in perl5
provides functions for generating lists

Provides

in lib/FAST/Bio/GapSeq.pm
in lib/FAST/Bio/Root/Exception.pm
in lib/FAST/Bio/Root/IO.pm
in lib/FAST/Bio/Root/Root.pm
in lib/FAST/Bio/Root/RootI.pm
in lib/FAST/Bio/Root/Version.pm
in lib/FAST/Bio/MySeqUtils.pm