Semi-local string comparison: algorithmic techniques and applications
release_a7i35a5bo5gexmadcacvnqstse
by
Alexander Tiskin
2009
Abstract
A classical measure of string comparison is given by the longest common
subsequence (LCS) problem on a pair of strings. We consider its generalisation,
called the semi-local LCS problem, which arises naturally in many
string-related problems. The semi-local LCS problem asks for the LCS scores for
each of the input strings against every substring of the other input string,
and for every prefix of each input string against every suffix of the other
input string. Such a comparison pattern provides a much more detailed picture
of string similarity than a single LCS score; it also arises naturally in many
string-related problems. In fact, the semi-local LCS problem turns out to be
fundamental for string comparison, providing a powerful and flexible
alternative to classical dynamic programming. It is especially useful when the
input to a string comparison problem may not be available all at once: for
example, comparison of dynamically changing strings; comparison of compressed
strings; parallel string comparison. The same approach can also be applied to
permutation strings, providing efficient solutions for local versions of the
longest increasing subsequence (LIS) problem, and for the problem of computing
a maximum clique in a circle graph. Furthermore, the semi-local LCS problem
turns out to have surprising connections in a few seemingly unrelated fields,
such as computational geometry and algebra of semigroups. This work is devoted
to exploring the structure of the semi-local LCS problem, its efficient
solutions, and its applications in string comparison and other related areas,
including computational molecular biology.
In text/plain
format
Archived Files and Locations
application/pdf 611.1 kB
file_msqonkqjlvehhggprsjeihckme
|
arxiv.org (repository) web.archive.org (webarchive) |
0707.3619v11
access all versions, variants, and formats of this works (eg, pre-prints)