Bio::DB::SeqFeature::Store::bdb Bio::DB::SeqFeature::Store::bdb can fetch and store objects from a BerkeleyDB.
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database Perl module perl store objects BerkeleyDB BerkeleyDB database

Bio::DB::SeqFeature::Store::bdb Description

Bio::DB::SeqFeature::Store::bdb can fetch and store objects from a BerkeleyDB. Bio::DB::SeqFeature::Store::bdb can fetch and store objects from a BerkeleyDB.Bioperl is a package of public domain Perl tools for computational molecular biology.All modules are in the Bio/ namespace, · Perl is for newbies and gives a functional interface to the main parts of the package· Seq is for Sequences (protein and DNA).· Bio::PrimarySeq is a plain sequence (sequence data + identifiers)· Bio::Seq is a PrimarySeq plus it has a Bio::Annotation::Collection and a Bio::SeqFeatureI objects attached.· Bio::Seq::RichSeq is all of the above plus it has slots for extra information specific to GenBank/EMBL/SwissProt files.· Bio::Seq::LargeSeq is for sequences which are too big for fitting into memory.· SeqIO is for reading and writing Sequences, it is a front end module for separate driver modules supporting the different sequence formats· SeqFeature· start/stop/strand annotations of sequences· Bio::SeqFeature::Generic is basic catchall· Bio::SeqFeature::Similarity a similarity sequence feature· Bio::SeqFeature::FeaturePair a sequence feature which is pairwise such as query/hit pairs· SearchIO is for reading and writing pairwise alignment reports like BLAST or FASTA· Search is where the alignment objects are defined· Bio::Search::Result::GenericResult is the result object (a blast query is a Result object)· Bio::Search::Hit::GenericHit is the Hit object (a query will have 0-> many hits in a database)· Bio::Search::HSP::GenericHSP is the High-scoring Segment Pair object defining the alignment(s) of the query and hit. · SimpleAlign is for multiple sequence alignments· AlignIO is for reading and writing multiple sequence alignment formats· Assembly provides the start of an infrastructure for assemblies and Assembly::IO IO converters for them· DB is the namespace for all the database query objects· Bio::DB::GenBank/GenPept are two modules which query NCBI entrez for sequences· Bio::DB::SwissProt/EMBL query various EMBL and SwissProt repositories for a sequences· Bio::DB::GFF is Lincoln Stein's fast, lightweight feature and sequence database which is the backend to his GBrowse system (see www.gmod.org)· Bio::DB::Flat is a fast implementation of the OBDA flat-file indexing system (cross-language and cross-platform supported by O|B|F projects see http://obda.open-bio.org).· Bio::DB::BioFetch/DBFetch for OBDA, Web (HTTP) access to remote databases.· Bio::DB::InMemoryCache/FileCache (fast local caching of sequences from remote dbs to speed up your access). · Bio::DB::Registry interface to the OBDA specification for remote data sources· Bio::DB::XEMBL SOAP access to sequence databases· Bio::DB::Biblio for access to remote bibliographic databases.· Annotation collection of annotation objects (comments, DBlinks, References, and misc key/value pairs)· Coordinate is a system for mapping between different coordinate systems such as DNA to protein or between assemblies.· Index is for locally indexed flatfiles with BerkeleyDB· Tools contains many miscellaneous parsers and function for different bioinformatics needs· Gene prediction parser (Genscan, MZEF, Grail, Genemark)· Annotation format (GFF)· simulate restriction enzyme cutting with RestrictionEnzyme· Enumerate codon tables and valid sequences symbols (CodonTable, IUPAC)· Phylogenetic program parsing (PAML, Molphy, Phylip)· Map genetic and physical map representations· Graphics render a sequence with its features or a sequence analysis result.· Structure· parse and represent protein structure data· TreeIO is for reading and writing Tree formats· Tree is the namespace for all the associated Tree objects· Bio::Tree::Tree is the basic tree object· Bio::Tree::Node are the nodes which make up the tree· Bio::Tree::Statistics is for computing statistics for a tree· Bio::Tree::TreeFunctionsI is where specific tree functions are implemented (like is_monophyletic and lca)· Bio::Biblio is where bibliographic data and database access objects are kept· Variation represent sequences with mutations and variations applied so one can compare and represent wild-type and mutation versions of a sequence.· Root, basic objects for the internals of BioperlRequirements:· Perl Requirements: · Perl

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