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2000
ACM
156views Algorithms» more  STOC 2000»
14 years 3 months ago
Near optimal multiple alignment within a band in polynomial time
Multiple sequence alignment is a fundamental problem in computational biology. Because of its notorious difficulties, aligning sequences within a constant band (c-diagonal) is a ...
Ming Li, Bin Ma, Lusheng Wang
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
BMCBI
2004
125views more  BMCBI 2004»
13 years 10 months ago
A fast algorithm for determining the best combination of local alignments to a query sequence
Background: Existing sequence alignment algorithms assume that similarities between DNA or amino acid sequences are linearly ordered. That is, stretches of similar nucleotides or ...
Gavin C. Conant, Andreas Wagner
DATESO
2007
157views Database» more  DATESO 2007»
14 years 10 days ago
Index-Based Approach to Similarity Search in Protein and Nucleotide Databases
When searching databases of nucleotide or protein sequences, finding a local alignment of two sequences is one of the main tasks. Since the sizes of available databases grow const...
David Hoksza, Tomás Skopal