Comparing Methods for Finding Gene Trap Sequences
Author Information
Author(s): Courtney A. Harper, Conrad C. Huang, Doug Stryke, Michiko Kawamoto, Thomas E. Ferrin, Patricia C. Babbitt
Primary Institution: University of California San Francisco
Hypothesis
How do different alignment programs perform in localizing gene trap sequences on the mouse genome?
Conclusion
All three programs performed well in localizing sequences to a general region of the genome, but there were significant differences in identifying exon boundaries.
Supporting Evidence
- BLAT correctly identified the vast majority of exon boundaries.
- SSAHA consistently reported the fewest false positives and was the fastest algorithm.
- MegaBLAST was comparable to BLAT in speed but was more prone to incorrect localizations.
Takeaway
Scientists compared three computer programs to see which one is best at finding where certain genes are located in the mouse genome, and they found that while all did a good job, some were better at finding specific parts of the genes.
Methodology
The study compared the performance of BLAT, SSAHA, and MegaBLAST alignment programs using a set of 3,369 gene trap sequence tags aligned to the mouse genome.
Limitations
The study's results may be affected by the quality of the sequence tags and the presence of pseudogenes.
Digital Object Identifier (DOI)
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