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» Comparison of Current BLAST Software on Nucleotide Sequences
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BIBE
2008
IEEE
142views Bioinformatics» more  BIBE 2008»
13 years 11 months ago
Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
— The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
Ashwin M. Aji, Wu-chun Feng
BIBE
2001
IEEE
13 years 9 months ago
An XML Application For Genomic Data Interoperation
As the eXtensible Markup Language (XML) becomes a popular or standard language for exchanging data over the Internet/Web, there are a growing number of genome Web sites that make ...
Kei-Hoi Cheung, Yang Liu, Anuj Kumar, Michael Snyd...
BMCBI
2008
99views more  BMCBI 2008»
13 years 5 months ago
Multiple organism algorithm for finding ultraconserved elements
Background: Ultraconserved elements are nucleotide or protein sequences with 100% identity (no mismatches, insertions, or deletions) in the same organism or between two or more or...
Scott Christley, Neil F. Lobo, Gregory R. Madey
ISMB
1997
13 years 6 months ago
SEALS: A System for Easy Analysis of Lots of Sequences
We present a system of programs designed to facilitate sequence analysis projects involving large amounts of data. SEALS (System for Easy Analysis of Lots of Sequences) is a logic...
D. Roland Walker, Eugene V. Koonin
BMCBI
2004
146views more  BMCBI 2004»
13 years 5 months ago
The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence
Background: The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) ...
Sierra D. Stoneberg Holt, Jason A. Holt