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Computational discovery of internal micro-exons

  1. Author:
    Volfovsky, N.
    Haas, B. J.
    Salzberg, S. L.

  2. Author Address

    NCI, Adv Biomed Comp Ctr, Frederick SAIC, Frederick, MD 21702 USA Inst Genomic Res, Rockville, MD 20850 USA Volfovsky N NCI, Adv Biomed Comp Ctr, Frederick SAIC, Frederick, MD 21702 USA
    1. Year: 2003
  2. Journal: Genome Research
    1. 13
    2. 6
    3. Pages: 1216-1221
  4. Type of Article: Article
  1. Abstract:

    Very short exons, also known as micro-exons, occur ill large numbers ill some eukaryotic genomes. Existing annotation tools have a limited ability to recognize these short sequences, which range ill length LIP to 25 bp. Here, we describe a computational method for the identification of micro-exons using near-perfect alignments between cDNA and genomic DNA sequences. Using this method, we detected 319 micro-exons ill 4 complete genomes, of which 224 were previously Unknown, human (170), the nematode Caenorhabditis elegans (4), tile fruit fly Drosophila melanogaster (14), and the mustard plant Arabidopsis thaliana (36). Comparison Of our computational method with popular cDNA alignment programs shows that the new algorithm is both efficient and accurate. The algorithm also aids in the discovery of micro-exon-skipping events and cross-species micro-exon conservation.

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