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» Alignment of Non-Overlapping Sequences
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BMCBI
2006
120views more  BMCBI 2006»
13 years 10 months ago
Optimizing amino acid substitution matrices with a local alignment kernel
Background: Detecting remote homologies by direct comparison of protein sequences remains a challenging task. We had previously developed a similarity score between sequences, cal...
Hiroto Saigo, Jean-Philippe Vert, Tatsuya Akutsu
ACL
2003
13 years 11 months ago
Word Sense Disambiguation Using Pairwise Alignment
In this paper, we proposed a new supervised word sense disambiguation (WSD) method based on a pairwise alignment technique, which is used generally to measure a similarity between...
Koichi Yamashita, Keiichi Yoshida, Yukihiro Itoh
BMCBI
2005
87views more  BMCBI 2005»
13 years 10 months ago
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related protei
Background: Profile-profile methods have been used for some years now to detect and align homologous proteins. The best such methods use information from the background distributi...
Tomas Ohlson, Arne Elofsson
TCBB
2008
95views more  TCBB 2008»
13 years 10 months ago
Solving the Problem of Trans-Genomic Query with Alignment Tables
Abstract-- The trans-genomic query (TGQ) problem -- enabling the free query of biological information, even across genomes -- is a central challenge facing bioinformatics. Solution...
Douglas Stott Parker Jr., Ruey-Lung Hsiao, Yi Xing...
RECOMB
2010
Springer
13 years 8 months ago
Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps
Chaining fragments is a crucial step in genome alignment. Existing chaining algorithms compute a maximum weighted chain with no overlaps allowed between adjacent fragments. In prac...
Raluca Uricaru, Alban Mancheron, Eric Rivals