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Unformatted text preview: Computational Biology, Part 6 Sequence Database Searching Robert F. Murphy Copyright © 1996-2005. Copyright All rights reserved. Sequence Analysis Tasks ⇒ Given a query sequence, search for similar sequences in a database sequences Global or Local? Both local and global alignment methods may be applied to database scanning, but local alignment methods are more useful since they do not make the assumption that the query protein and database sequence are of similar length. Efficient database searching methods s Dynamic programming requires order N2L computations (where N is size of the query sequence and L is the size of the database) sequence s Given size of databases, more efficient Given methods needed methods “Hit and extend” sequence searching s Problem: Too many calculations “wasted” Problem: by comparing regions that have nothing in common common s Initial insight: Regions that are similar Initial similar between two sequences are likely to share short stretches that are identical identical s Basic method: Look for similar regions only Basic near short stretches that match exactly exactly “Hit and extend” sequence searching s We define a word (or k-tuple) size that is We word -tuple) the minimum number of exact “letter” matches that must occur before we do any further comparison or alignment further s How do we find all of the occurences of How matching words between a se...
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This note was uploaded on 01/13/2012 for the course BIO 101 taught by Professor Staff during the Fall '10 term at DePaul.

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