ESTGenes: Alternative Splicing From ESTs in Ensembl (original) (raw)

1. Eduardo Eyras1,
2. Mario Caccamo,
3. Val Curwen, and
4. Michele Clamp
5. The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

Abstract

We describe a novel algorithm for deriving the minimal set of nonredundant transcripts compatible with the splicing structure of a set of ESTs mapped on a genome. Sets of ESTs with compatible splicing are represented by a special type of graph. We describe the algorithms for building the graphs and for deriving the minimal set of transcripts from the graphs that are compatible with the evidence. These algorithms are part of the Ensembl automatic gene annotation system, and its results, using ESTs, are provided at www.ensembl.org as ESTgenes for the mosquito, Caenorhabditis briggsae, C. elegans, zebrafish, human, mouse, and rat genomes. Here we also report on the results of this method applied to the human and mouse genomes.

Footnotes

• [Supplemental material is available online at www.genome.org.\]

• ↵2 Known genes are supported by a cDNA or a protein and have a LocusLink or GDB entry, whereas Novel-CDS genes are supported by spliced ESTs or by similarity to another gene and have an unambiguous open reading frame.

• Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1862204.

• ↵1 Corresponding author. E-MAIL eae{at}sanger.ac.uk; FAX 44-1223-494919.

• • Accepted December 18, 2003.
  • Received August 8, 2003.

• Cold Spring Harbor Laboratory Press

•