Search results for "distribution:Bio-Variation HEIKKI"
Bio::Variation::IO - Handler for sequence variation IO Formats
Bio::Variation::IO is a handler module for the formats in the Variation IO set (eg, Bio::Variation::IO::flat). It is the officially sanctioned way of getting at the format objects, which most people should use. The structure, conventions and most of ...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
Bio::Variation::Allele - Sequence object with allele-specific attributes
List of alleles describe known sequence alternatives in a variable region. Alleles are contained in Bio::Variation::VariantI complying objects. See Bio::Variation::VariantI for details. Bio::Varation::Alleles are PrimarySeqI complying objects which c...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
Bio::Variation::IO::xml - XML sequence variation input/output stream
This object can transform Bio::Variation::SeqDiff objects to and from XML file databases. The XML format, although consistent, is still evolving. The current DTD for it is at <http://www.ebi.ac.uk/mutations/DTDE/seqDiff.dtd>....
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
Bio::Variation::IO::flat - flat file sequence variation input/output stream
This object can transform Bio::Variation::SeqDiff objects to and from flat file databases....
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
Bio::Variation::SeqDiff - Container class for mutation/variant descriptions
SeqDiff stores Bio::Variation::VariantI object references and descriptive information common to all changes in a sequence. Mutations are understood to be any kind of sequence markers and are expected to occur in the same chromosome. See Bio::Variatio...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
Bio::Variation::AAChange - Sequence change class for polypeptides
The instantiable class Bio::Variation::RNAChange describes basic sequence changes at polypeptide level. It uses methods defined in superclass Bio::Variation::VariantI, see Bio::Variation::VariantI for details. If the variation described by a AAChange...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
Bio::Variation::VariantI - Sequence Change SeqFeature abstract class
This superclass defines common methods to basic sequence changes. The instantiable classes Bio::Variation::DNAMutation, Bio::Variation::RNAChange and Bio::Variation::AAChange use them. See Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and B...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
Bio::Variation::RNAChange - Sequence change class for RNA level
The instantiable class Bio::Variation::DNAMutation describes basic sequence changes at RNA molecule level. It uses methods defined in superclass Bio::Variation::VariantI. See Bio::Variation::VariantI for details. You are normally expected to create a...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
Bio::Variation::DNAMutation - DNA level mutation class
The instantiable class Bio::Variation::DNAMutation describes basic sequence changes in genomic DNA level. It uses methods defined in superclass Bio::Variation::VariantI. See Bio::Variation::VariantI for details. If the variation described by a DNAMut...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
Bio::Variation::AAReverseMutate - point mutation and codon information from single amino acid changes
Bio::Variation::AAReverseMutate objects take in reference and mutated amino acid information and deduces potential point mutations at RNA level leading to this change. The choice can be further limited by letting the object know what is the the codon...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC
bp_flanks - finding flanking sequences for a variant in a sequence position
This script allows you to extract a subsequence around a region of interest from an existing sequence. The output if fasta formatted sequence entry where the header line contains additional information about the location....
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC