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

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 probl...

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Bibliographic Details
Published inGenome research Vol. 8; no. 9; pp. 967 - 974
Main Authors Florea, L, Hartzell, G, Zhang, Z, Rubin, G M, Miller, W
Format Journal Article
LanguageEnglish
Published United States Cold Spring Harbor Laboratory Press 01.09.1998
Subjects
Algorithms
Animals
Computational Biology
DNA - genetics
DNA, Complementary - genetics
Drosophila melanogaster - genetics
Expressed Sequence Tags
Genome
Genome Methods
Humans
Mice
RNA, Messenger - genetics
Sequence Alignment - methods
Sequence Homology, Nucleic Acid
Software
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Summary: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.
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Corresponding author.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.8.9.967