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BMCBI
2006
143views more  BMCBI 2006»
14 years 11 months ago
Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
Background: The estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of t...
Christophe Dessimoz, Manuel Gil, Adrian Schneider,...
ISMB
1996
15 years 1 months ago
Compact Encoding Strategies for DNA Sequence Similarity Search
Determining whether two DNA sequences are similar is an essential component of DNA sequence analysis. Dynamic programming is the algorithm of choice if computational time is not t...
David J. States, Pankaj Agarwal
ICDE
2004
IEEE
105views Database» more  ICDE 2004»
16 years 1 months ago
SPINE: Putting Backbone into String Indexing
The indexing technique commonly used for long strings, such as genomes, is the suffix tree, which is based on a vertical (intra-path) compaction of the underlying trie structure. ...
Naresh Neelapala, Romil Mittal, Jayant R. Haritsa
BMCBI
2008
128views more  BMCBI 2008»
14 years 11 months ago
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor bindin
Background: Biologically active sequence motifs often have positional preferences with respect to a genomic landmark. For example, many known transcription factor binding sites (T...
Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mari...
RIVF
2008
15 years 1 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