Uses of Package
util.bio.annotation

Packages that use util.bio.annotation

expr	Classes and tools related to expression array analysis.
gata.geneGlyphs	For representing annotation, scale bars, and generic tracks.
gata.main	Main app, utility, and params for GATAPlotter.
trans.anno	For associating intervals, binding regions, and binding peaks with GFF annotation.
trans.main	Principle classes and scripts used in TiMAT2 analysis.
trans.roc	For manipulating the BAC dmel spike in data and generating ROC curves.
util.bio.annotation	For representing gene annotation.
util.bio.parsers	Parsers and extractors, fasta, quality, text, gff....
util.bio.parsers.gff	GFF2 and GFF3 parsers.

Classes in util.bio.annotation used by expr

Coordinates
Base class for holding info about a genomic coordinate.

Classes in util.bio.annotation used by gata.geneGlyphs

GeneRep
A GeneRep resentation contains a genomic sequence designating a gene broken into various segments.

GenericFeature
Class to hold user defined gff items like CRMs, enhancers, unpublished single track notation.

TransGroup
A TransGroup describes a product derived from a GeneGroup contains one transcript, possibly a translation, and a possibly a set of exons.

Classes in util.bio.annotation used by gata.main

ExonIntron
ExonIntron info.

Classes in util.bio.annotation used by trans.anno

GeneGroup
A GeneGroup is the top organizing level of a "Gene".

Classes in util.bio.annotation used by trans.main

ExonIntron
ExonIntron info.

Classes in util.bio.annotation used by trans.roc

GeneGroup
A GeneGroup is the top organizing level of a "Gene".

Classes in util.bio.annotation used by util.bio.annotation

Coordinates
Base class for holding info about a genomic coordinate.

ExonIntron
ExonIntron info.

GeneGroup
A GeneGroup is the top organizing level of a "Gene".

GeneRep
A GeneRep resentation contains a genomic sequence designating a gene broken into various segments.

Transcript
Transcript relevant information, mRNA.

TransGroup
A TransGroup describes a product derived from a GeneGroup contains one transcript, possibly a translation, and a possibly a set of exons.

Translation
Translation specific information, protein but referenced with genomic coordinates thus some bits code for protein, some don't physically exist.

Classes in util.bio.annotation used by util.bio.parsers

ExonIntron
ExonIntron info.

Classes in util.bio.annotation used by util.bio.parsers.gff

GeneGroup
A GeneGroup is the top organizing level of a "Gene".