A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence

  1. Liliana Florea1,
  2. George Hartzell2,
  3. Zheng Zhang1,
  4. Gerald M. Rubin2, and
  5. Webb Miller1,3
  1. 1Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 USA; 2Drosophila Genome Center, Berkeley, California 94720-3200 USA

Abstract

We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small number of sequencing errors. A freely available computer program, described herein, solves the problem for a 100-kb genomic sequence in a few seconds on a workstation.

Footnotes

  • ↵3 Corresponding author.

  • E-MAIL webb{at}cse.psu.edu; FAX (814) 865-3176.

    • Received May 18, 1998.
    • Accepted July 21, 1998.
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  1. doi: 10.1101/gr.8.9.967 Genome Res. 8: 967-974 Cold Spring Harbor Laboratory Press

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