Assignment 1

Assignment 1 - AI AL AS IA II IL IS LA LI LL LS SA SI SL SS...

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Introduction to Bioinformatics / Elements of Bioinformatics Assignment 1 Due: March 17, 2009 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
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Unformatted text preview: AI AL AS IA II IL IS LA LI LL LS SA SI SL SS 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 Positions of matching word in query AS SS 4 SL LA AI IA AI IA C) Extend to the left and right of the word pairs that contain SL in the database sequence. a) Find the high scoring alignments if a maximum drop-off threshold of 2 is used. b) Find the high scoring alignments if a maximum drop-off threshold of 4 is used....
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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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