Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction

  1. Serafim Batzoglou1,4,7,
  2. Lior Pachter2,7,
  3. Jill P. Mesirov3,
  4. Bonnie Berger1,4,6, and
  5. Eric S. Lander3,5,6
  1. 1Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA; 2Department of Mathematics, University of California Berkeley, Berkeley, California 94720 USA; 3Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142 USA; 4Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA; 5Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA

Abstract

We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of similarity in the number, size and sequence of exons and introns. We then developed an approach for recognizing genes within such orthologous regions by first aligning the regions using an iterative global alignment system and then identifying genes based on conservation of exonic features at aligned positions in both species. The alignment and gene recognition are performed by new programs calledGLASS and ROSETTA, respectively.ROSETTA performed well at exact identification of coding exons in 117 orthologous pairs tested.

Footnotes

  • ↵7 S.B. and L.P. contributed equally to this work.

  • ↵6 Corresponding author.

  • E-MAIL: lander{at}wi.mit.edu; FAX (617) 252-1902.

    • Received February 15, 2000.
    • Accepted May 2, 2000.
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  1. doi: 10.1101/gr.10.7.950 Genome Res. 10: 950-958 Cold Spring Harbor Laboratory Press

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