A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence (original) (raw)
- Liliana Florea1,
- George Hartzell2,
- Zheng Zhang1,
- Gerald M. Rubin2, and
- Webb Miller1,3
- 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.
Cold Spring Harbor Laboratory Press