ESTGenes: alternative splicing from ESTs in Ensembl

Genome Res. 2004 May;14(5):976-87. doi: 10.1101/gr.1862204.


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 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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.
  • Validation Study

MeSH terms

  • Alternative Splicing / genetics*
  • Animals
  • Caenorhabditis / genetics
  • Caenorhabditis elegans / genetics
  • Computational Biology
  • Culicidae / genetics
  • DNA, Helminth / genetics
  • Expressed Sequence Tags*
  • Genes
  • Genes, Helminth
  • Genes, Insect
  • Humans
  • Mice
  • Predictive Value of Tests
  • Rats
  • Reproducibility of Results
  • Software*
  • Transcription, Genetic
  • Zebrafish / genetics


  • DNA, Helminth