ESTGenes: alternative splicing from ESTs in Ensembl.
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.
Eyras
Eduardo
E
The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. eae@sanger.ac.uk
Caccamo
Mario
M
Curwen
Val
V
Clamp
Michele
M
D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D002107:Caenorhabditis / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics; D019295:Computational Biology; D009033:Culicidae / Q000235:genetics; D018509:DNA, Helminth / Q000235:genetics; D020224:Expressed Sequence Tags; D005796:Genes; D017238:Genes, Helminth; D017344:Genes, Insect; D006801:Humans; D051379:Mice; D011237:Predictive Value of Tests; D051381:Rats; D015203:Reproducibility of Results; D012984:Software; D014158:Transcription, Genetic; D015027:Zebrafish / Q000235:genetics
D018509:DNA, Helminth