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» Sequence Database Search Using Jumping Alignments
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BMCBI
2007
164views more  BMCBI 2007»
15 years 3 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
ITNG
2006
IEEE
15 years 9 months ago
Evaluating Parallel Computing Systems in Bioinformatics
The utilization of parallel processing in bioinformatics is a relatively new development, and wide spread use of parallel processing in this domain has been limited by the availab...
Erik S. Gough, Michael D. Kane
BIOCOMP
2009
15 years 4 months ago
Improving Remote Homology Detection Using Sequence Properties and Position Specific Scoring Matrices
Current biological sequence comparison tools frequently fail to recognize matches between homologs when sequence similarity is below the twilight zone of less than 25% sequence id...
Gina Cooper, Michael L. Raymer
CPM
2001
Springer
72views Combinatorics» more  CPM 2001»
15 years 7 months ago
Tandem Cyclic Alignment
We present a solution for the following problem. Given two sequences X = x1x2 · · · xn and Y = y1y2 · · · ym, n ≤ m, find the best scoring alignment of X = Xk [i] vs Y ove...
Gary Benson
ICCSA
2004
Springer
15 years 8 months ago
A Sequence-Focused Parallelisation of EMBOSS on a Cluster of Workstations
Abstract. A number of individual bioinformatics applications (particularly BLAST and other sequence searching methods) have recently been implemented over clusters of workstations ...
Karl Podesta, Martin Crane, Heather J. Ruskin