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» Alignment of Non-Overlapping Sequences
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BMCBI
2005
138views more  BMCBI 2005»
13 years 10 months ago
Detailed protein sequence alignment based on Spectral Similarity Score (SSS)
Background: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine ali...
Kshitiz Gupta, Dina Thomas, S. V. Vidya, K. V. Ven...
BIBM
2010
IEEE
156views Bioinformatics» more  BIBM 2010»
13 years 8 months ago
Truncation of protein sequences for fast profile alignment with application to subcellular localization
We have recently found that the computation time of homology-based subcellular localization can be substantially reduced by aligning profiles up to the cleavage site positions of s...
Man-Wai Mak, Wei Wang, Sun-Yuan Kung
CPM
2006
Springer
112views Combinatorics» more  CPM 2006»
14 years 2 months ago
Local Alignment of RNA Sequences with Arbitrary Scoring Schemes
Abstract. Local similarity is an important tool in comparative analysis of biological sequences, and is therefore well studied. In particular, the Smith-Waterman technique and its ...
Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren...
ICDM
2008
IEEE
106views Data Mining» more  ICDM 2008»
14 years 4 months ago
Boosting Relational Sequence Alignments
The task of aligning sequences arises in many applications. Classical dynamic programming approaches require the explicit state enumeration in the reward model. This is often impr...
Andreas Karwath, Kristian Kersting, Niels Landwehr
DOCENG
2006
ACM
14 years 4 months ago
Fast and simple XML tree differencing by sequence alignment
With the advent of XML we have seen a renewed interest in methods for computing the difference between trees. Methods that include heuristic elements play an important role in pr...
Tancred Lindholm, Jaakko Kangasharju, Sasu Tarkoma