A computer program for aligning a cDNA sequence with a genomic DNA sequence

Genome Res. 1998 Sep;8(9):967-74. doi: 10.1101/gr.8.9.967.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Animals
  • Computational Biology
  • DNA / genetics*
  • DNA, Complementary / genetics*
  • Drosophila melanogaster / genetics
  • Expressed Sequence Tags
  • Genome*
  • Humans
  • Mice
  • RNA, Messenger / genetics
  • Sequence Alignment / methods*
  • Sequence Homology, Nucleic Acid
  • Software*


  • DNA, Complementary
  • RNA, Messenger
  • DNA