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Showing content from https://doi.org/10.1101/gr.8.9.967 below:

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

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.

• ↵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

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