Search results for "distribution:BioPerl HEIKKI"
Bio::Range - Pure perl RangeI implementation
This provides a pure perl implementation of the BioPerl range interface. Ranges are modeled as having (start, end, length, strand). They use Bio-coordinates - all points >= start and <= end are within the range. End is always greater-than or equal-to...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::RangeI - Range interface
This provides a standard BioPerl range interface that should be implemented by any object that wants to be treated as a range. This serves purely as an abstract base class for implementers and can not be instantiated. Ranges are modeled as having (st...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::WebAgent - A base class for Web (any protocol) access
This abstract superclass is a subclass of LWP::UserAgent which allows protocol independent access of remote locations over the Net. It takes care of error handling, proxies and various net protocols. BioPerl classes accessing the net should inherit f...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqUtils - Additional methods for PrimarySeq objects
This class is a holder of methods that work on Bio::PrimarySeqI- compliant sequence objects, e.g. Bio::PrimarySeq and Bio::Seq. These methods are not part of the Bio::PrimarySeqI interface and should in general not be essential to the primary functio...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::Meta - Generic superclass for sequence objects with residue-based meta information
This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are Bio::LocatableSeq objects with additional methods to store that meta information. See Bio::LocatableSeq and Bio::Seq::MetaI. Th...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::scf - .scf file input/output stream
This object can transform .scf files to and from Bio::Seq::SequenceTrace objects. Mechanisms are present to retrieve trace data from scf files....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::MetaI - Interface for sequence objects with residue-based meta information
This class defines an abstract interface for basic residue-based meta information. Examples of this kind of meta data are secondary structures (RNA and protein), protein hydrophobicity assignments, or other alternative alphabets for polypeptides, seq...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_oligo_count - oligo count and frequency
This scripts counts occurrence and frequency for all oligonucleotides of given length. It can be used to determine what primers are useful for frequent priming of nucleic acid for random labeling. Note that this script could be run by utilizing the c...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::DBFetch - Database object for retrieving using the dbfetch script
Allows the dynamic retrieval of entries from databases using the dbfetch script at EBI: http://www.ebi.ac.uk/cgi-bin/dbfetch. In order to make changes transparent we have host type (currently only ebi) and location (defaults to ebi) separated out. Th...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SimpleAlign - Multiple alignments held as a set of sequences
SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipula...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::Quality - Implementation of sequence with residue quality and trace values
This object stores base quality values together with the sequence string. The implementation is based on Bio::Seq::Meta::Array. qual() and trace() are base methods to store and retrieve information that have extensions to retrieve values as a scalar ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Align::AlignI - An interface for describing sequence alignments.
This interface describes the basis for alignment objects....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::LargeSeqI - Interface class for sequences that cache their residues in a temporary file
The interface class defines a group of sequence classes that do not keep their sequence information in memory but store it in a file. This makes it possible to work with very large files even with limited RAM. The most important consequence of file c...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::nexus - NEXUS format sequence input/output stream
This object can transform Bio::Align::AlignI objects to and from NEXUS data blocks. See method documentation for supported NEXUS features....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::genbank - GenBank sequence input/output stream
This object can transform Bio::Seq objects to and from GenBank flat file databases. There is some flexibility here about how to write GenBank output that is not fully documented. Optional functions _show_dna() (output only) shows the dna or not _post...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::phylip - PHYLIP format sequence input/output stream
This object can transform Bio::SimpleAlign objects to and from PHYLIP format. By default it works with the interleaved format. By specifying the flag -interleaved => 0 in the initialization the module can read or write data in sequential format. Read...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::gbdriver - GenBank handler-based push parser
This object can transform Bio::Seq objects to and from GenBank flat file databases. The key difference between this parser and the tried-and-true Bio::SeqIO::genbank parser is this version separates the parsing and data manipulation into a 'driver' m...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::SeqStats - Object holding statistics for one particular sequence
Bio::Tools::SeqStats is a lightweight object for the calculation of simple statistical and numerical properties of a sequence. By "lightweight" I mean that only "primary" sequences are handled by the object. The calling script needs to create the app...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DBLinkContainerI - Abstract interface for any object wanting to use database cross references
This interface defines the functions one can expect for any object wanting to use database cross-references. This class does not actually provide any implementation, it just provides the definitions of what methods one can call. The database cross-re...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::metafasta - metafasta sequence input/output stream
This object can transform Bio::Seq::Meta objects to and from metafasta flat file databases. For sequence part the code is an exact copy of Bio::SeqIO::fasta module. The only added bits deal with meta data IO. The format of a metafasta file is >test A...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC