Assignment 1_ans

Assignment 1_ans - Introduction to Bioinformatics /...

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Introduction to Bioinformatics / Elements of Bioinformatics Assignment 1 - Answers Use the one-hit BLAST method to find high scoring alignments between query sequence q = SILSALIISL and database sequence d = ASSLAIAIA. A) Make a table listing all possible 2-letter neighborhood words (i.e. wordsize = 2) from the query sequence. You only need to consider residues A, I, L, S in this case. Determine the positions in the query sequence where the neighborhood words match the query sequence using a threshold T = 5 and scoring matrix BLOSUM62: Neighborhood words Positions in query sequence when T = 5 AA 4 AI 1, 5 AL 5, 9 AS IA 8 II 2, 6, 7 IL 2, 7 IS 3, 8 LA 3 LI 6, 7 LL 2, 6 LS 3, 8 SA 4 SI 1, 9 SL 1, 5, 9 SS 4 A I L S A 4 -1 -1 1 I -1 4 2 -2 L -1 2 4 -2 S 1 -2 -2 4 B) For each 2-letter word from the database sequence, find matching word in the neighborhood words table. Record for each 2-letter word the positions of the matching words in the query sequence: 2-letter words from database sequence
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This note was uploaded on 07/29/2010 for the course BIOC BIOC1805 taught by Professor Dr.brianwong during the Summer '09 term at HKU.

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Assignment 1_ans - Introduction to Bioinformatics /...

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