ASSIGNMENT 2 cont.

Self study at S - star

i.e.  Comparative Genomics

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Method ? Input: translation of all ORFs in complete genomes. One genome as query, and the others are references. ? Progedure: 1. The query set is compared against itself using BLASTP; Pairwise sequences similarities are recorded in a binary matrix T. - mask composionally biased regions (CAST) - Use Smith –Waterman to symmetrify the matrix 2. The query set is compared against reference set using BLASTP; Pairwise sequences similarities are recorded in binary matrix Y. 3. For each entry C in reference set, collect pair (A,B) from the query set where both A and B are similar to C. - Look up (A,B) in matrix T - If (A,B) is null in T, run Smith – Waterman to confirm dissimilarity. - If dissimilar, collect (A,B) as candidates for fusion event.