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» Choosing the best heuristic for seeded alignment of DNA sequ...
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BIBM
2009
IEEE
118views Bioinformatics» more  BIBM 2009»
13 years 8 months ago
Inexact Local Alignment Search over Suffix Arrays
We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may conta...
Mohammadreza Ghodsi, Mihai Pop
BMCBI
2007
164views more  BMCBI 2007»
13 years 4 months ago
SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA
Background: Computational methods to predict transcription factor binding sites (TFBS) based on exhaustive algorithms are guaranteed to find the best patterns but are often limite...
Fathi Elloumi, Martha Nason