Sequence Alignment
October 14 , 2008
Homework Assignment Number 4
Align two of your protein sequences from assignment 2 using Bestfit or EMBOSS Pairwise Alignment tool. Repeat the alignment with the same two sequences using the NORMALIZED gap penalties of 1, 2, 4, 8, 16 and 32 (you mays use ABSOLUTE gap penalties 4, 8, 16, 32, and 64 for programs that require those). Keep the ratio of the gap penalty to the gap extension penalty the same in all cases. It is important that the two proteins be rather distant from each other (30 to 60% identity max) so as to have gaps in their alignments.
The easiest way to find such a pair of proteins is to use one protein as a query in a BLASTP search on the NCBI web page (NCBI BLAST Home Page) and then choose a protein 30% to 60% identical from the proteins in the BLAST output.
Examine the alignments and describe the effect of raising the gap penalty on the number and arrangements of gaps seen in these alignments. Mention which of the alignments has the highest overall score (or quality) and are the gaps arranged in a biologically significant manner. Send the results to
homework218@cmgm.Stanford.EDU.
Due October 21, 2008