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Basic local alignment search tool.
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP)Expand
Optimal alignments in linear space
The goal of this paper is to give Hirschberg's idea the visibility it deserves by developing a linear-space version of Gotoh's algorithm, which accommodates affine gap penalties. Expand
Automatic Generation of Floating-Point Test Data
Two examples, a matrix factorization subroutine and a sorting method, illustrate the types of data generation problems that can be successfully treated with numerical maximization techniques. Expand
Sequence comparison with concave weighting functions.
Two algorithms based on the ‘candidate list paradigm’ first used by Waterman (1984) are presented, one of which computes significantly more parsimonious candidate lists than Waterman's method. Expand
A file comparison program
A simple method for computing a shortest sequence of insertion and deletion commands that converts one given file to another, which is particularly efficient when the difference between the two files is small compared to the files' lengths. Expand
Approximate matching of regular expressions
Given a sequenceA and regular expressionR, theapproximate regular expression matching problem is to find a sequence matchingR whose optimal alignment withA is the highest scoring of all suchExpand
Approximate matching of regular expressions.
An algorithm to solve the problem in time O(MN), where M and N are the lengths of A and R, and requires only O(N) space to deliver just the score of the best alignment, superior to an earlier algorithm by Wagner and Seiferas. Expand