LecturesPart06

Database x could scan sequence a word at a time but

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Unformatted text preview: quence and a database? database? x Could scan sequence a word at a time, but this Could is order L (size of database) is Word searching - hashing s Solution: Use a precomputed table that lists Solution: where in the database each possible word occurs occurs x Generation of the table is of order L (size of database) but use of the table is of order N (size use of query sequence) of s The computer science term for this approach The is hashing hashing Hashing s Hashing x Hashing Table of size 10 x Hashing function H(x) = x mod 10 x Applet: http://www.engin.umd.umich.edu/CIS/course.des/cis x Insertion & Search s (Demonstration A10) FASTA s Heavily used for searching databases until Heavily advent of BLAST (see below) advent s Inputs x k (word or k-tuple) size (word x similarity matrix s Compares query sequence pairwise with Compares each sequence in the database each FASTA method s The initial step in the algorithm is to identify all exact matches of length k (k– tuples) or greater between the two sequences. FASTA method 1. Find diagonals (paired pieces from each 1. sequence without gaps) that have the highest density of common wor...
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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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