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RIVF
2008
13 years 9 months ago
Speeding up subset seed algorithm for intensive protein sequence comparison
Abstract--Sequence similarity search is a common and repeated task in molecular biology. The rapid growth of genomic databases leads to the need of speeding up the treatment of thi...
Van Hoa Nguyen, Dominique Lavenier
BMCBI
2005
93views more  BMCBI 2005»
13 years 7 months ago
Multiple sequence alignment accuracy and evolutionary distance estimation
Background: Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pai...
Michael S. Rosenberg
IPPS
2008
IEEE
14 years 2 months ago
Ordered index seed algorithm for intensive DNA sequence comparison
This paper presents a seed-based algorithm for intensive DNA sequence comparison. The novelty comes from the way seeds are used to efficiently generate small ungapped alignments ...
Dominique Lavenier
SISAP
2008
IEEE
166views Data Mining» more  SISAP 2008»
14 years 1 months ago
Approximate Similarity Search in Genomic Sequence Databases Using Landmark-Guided Embedding
Similarity search in sequence databases is of paramount importance in bioinformatics research. As the size of the genomic databases increases, similarity search of proteins in the...
Ahmet Sacan, Ismail Hakki Toroslu
UAI
2004
13 years 9 months ago
Blind Construction of Optimal Nonlinear Recursive Predictors for Discrete Sequences
We present a new method for nonlinear prediction of discrete random sequences under minimal structural assumptions. We give a mathematical construction for optimal predictors of s...
Cosma Rohilla Shalizi, Kristina Lisa Shalizi