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» Optimal detection of sequence similarity by local alignment
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IPPS
2007
IEEE
14 years 1 months ago
Reconfigurable Architecture for Biological Sequence Comparison in Reduced Memory Space
DNA sequence alignment is a very important problem in bioinformatics. The algorithm proposed by Smith-Waterman (SW) is an exact method that obtains optimal local alignments in qua...
Azzedine Boukerche, Jan Mendonca Correa, Alba Cris...
GECCO
2003
Springer
129views Optimization» more  GECCO 2003»
14 years 25 days ago
Evolutionary Two-Dimensional DNA Sequence Alignment
This article presents a model for DNA sequence alignment. In our model, a finite state automaton writes two-dimensional maps of nucleotide sequences. An evolutionary method for se...
Edgar E. Vallejo, Fernando Ramos
BMEI
2008
IEEE
14 years 2 months ago
A New Approach for Tree Alignment Based on Local Re-Optimization
Multiple sequence alignment is the most fundamental task in bioinformatics and computational biology. In this paper, we present a new algorithm to conduct multiple sequences align...
Feng Yue, Jijun Tang
NAR
2010
107views more  NAR 2010»
13 years 2 months ago
PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences
Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attun...
Satish Chikkagoudar, Dennis R. Livesay, Usman Rosh...
BMCBI
2007
126views more  BMCBI 2007»
13 years 7 months ago
Multiple non-collinear TF-map alignments of promoter regions
Background: The analysis of the promoter sequence of genes with similar expression patterns is a basic tool to annotate common regulatory elements. Multiple sequence alignments ar...
Enrique Blanco, Roderic Guigó, Xavier Messe...