BLAST) Stephen Altschul, Warren Gish, Webb Miller, Eugene Myers, David Lipman

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Basic Local Alignment Search Tool (BLAST) Stephen Altschul, Warren Gish, Webb Miller, Eugene Myers, David Lipman Journal of Molecular Biology 1990 Presented for MBB752 Brian Dunican January 28, 2009 The Problem • Dynamic programming algorithms take too long when applied to large databases • Also these algorithms maximize similarity – InserQons – Deleons – Replacements • Example Needleman and Wunsch BLAST • Similarity measure is based on well defined mutaQon scores (PAM120) – OpQmizaQon of this measure approximates the results of dynamic programming algorithm • “Detect weak but biologically significant sequence similariQes, and is more than an order of magnitude faster” Methods • Matrix of Similarity – Proteins: similar +, dissimilar – (PAM120) – DNA: idenQQes +5, mismatches -4 • Units of Maximal Segment Pair (MSP) – Score can not be increased by shortening or lengthening the segment pair • BLAST seeks the highest MSP score (>=S) Method • ComputaQonally intensive to scan the database for all w-meres in search of S • Define a threshold value, T , as the lower bound for further analysis. • Database is searched for all words (w-meres) which can equal T. – Two steps • From matches with score >= T, dynamic programming is used to determine MSP – Traces out from hit to maximize score Method Matches we care about S Matches worth evaluaQng Score T Waste of Qme Parameters • The chance exists the a random sequence will exceed the S score (1) M and N are the length of the compared strings S is the arbitrary score K and lambda are coefficients Parameters • Used equaQon (1) to determine w and T parameters Time Constraints • Compile list of words that can score T from query • Scan database for matches to T-scoring words • Extend all hits to seek MSPs higher than S • Increasing w decreases Qme spent on step 3. • Make w too high and step one is limiQng factor Performance • Against real proteins – Woolly monkey myoglobin (w=4, t=17) • Actual: missed 43 MSPs with a 50>S>80 • Expected: miss 24 of 178 – Mouse immunoglobulin precursor V region • Actual: missed 2 with a 45>S>65 • Expected: miss 8 of 33 • Lost out in the monkey due to the uniform paern of conservaon • Expect that on average Blast will outperform the random model. Notes on Speed • Proteins: 500,00 residues/s • DNA: 2,000,000 bases/s .

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