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BMCBI
2005
125views more  BMCBI 2005»
13 years 7 months ago
DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment
Background: We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous ver...
Amarendran R. Subramanian, Jan Weyer-Menkhoff, Mic...
SC
2005
ACM
14 years 1 months ago
ClawHMMER: A Streaming HMMer-Search Implementation
The proliferation of biological sequence data has motivated the need for an extremely fast probabilistic sequence search. One method for performing this search involves evaluating...
Daniel Reiter Horn, Mike Houston, Pat Hanrahan
BMCBI
2007
143views more  BMCBI 2007»
13 years 7 months ago
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules
Background: In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular ...
Yair Horesh, Tirza Doniger, Shulamit Michaeli, Ron...
BMCBI
2005
97views more  BMCBI 2005»
13 years 7 months ago
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data
Background: As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum e...
Roald Rossnes, Ingvar Eidhammer, David A. Liberles
LION
2009
Springer
114views Optimization» more  LION 2009»
14 years 2 months ago
Substitution Matrices and Mutual Information Approaches to Modeling Evolution
Abstract. Substitution matrices are at the heart of Bioinformatics: sequence alignment, database search, phylogenetic inference, protein family classication are based on Blosum, P...
Stephan Kitchovitch, Yuedong Song, Richard C. van ...