A name, presumably unique within a gene dataset, of a Gene
Common names for the gene, possibly shared with other genes (for historical or ad hoc reasons)
The strand of the Gene (this is from data, not derived from the Transcripts' strand(s), and we leave open the possibility that a single Gene will have Transcripts in _both_ directions, e.g. anti-sense transcripts)
The Transcripts that are part of this gene model
A name, presumably unique within a gene dataset, of a Gene
Common names for the gene, possibly shared with other genes (for historical or ad hoc reasons)
Finds the union of all the locations of the transcripts for this gene, across all the reference sequences indicates by the transcripts themselves.
Finds the union of all the locations of the transcripts for this gene, across all the reference sequences indicates by the transcripts themselves.
A Seq of ReferenceRegions
The strand of the Gene (this is from data, not derived from the Transcripts' strand(s), and we leave open the possibility that a single Gene will have Transcripts in _both_ directions, e.
The strand of the Gene (this is from data, not derived from the Transcripts' strand(s), and we leave open the possibility that a single Gene will have Transcripts in _both_ directions, e.g. anti-sense transcripts)
The Transcripts that are part of this gene model
A 'gene model' is a small, hierarchical collection of objects: Genes, Transcripts, and Exons. Each Gene contains a collection of Transcripts, and each Transcript contains a collection of Exons, and together they describe how the genome is transcribed and translated into a family of related proteins (or other RNA products that aren't translated at all).
This review, Gerstein et al. "What is a gene, post-ENCODE? History and updated definition" Genome Research (2007) http://genome.cshlp.org/content/17/6/669.full
is a reasonably good overview both of what the term 'gene' has meant in the past as well as where it might be headed in the future.
Here, we aren't trying to answer any of these questions about "what is a gene," but rather to provide the routines necessary to _re-assemble_ hierarchical models of genes that have been flattened into features (GFF, GTF, or BED)
A name, presumably unique within a gene dataset, of a Gene
Common names for the gene, possibly shared with other genes (for historical or ad hoc reasons)
The strand of the Gene (this is from data, not derived from the Transcripts' strand(s), and we leave open the possibility that a single Gene will have Transcripts in _both_ directions, e.g. anti-sense transcripts)
The Transcripts that are part of this gene model