BMD550 bioinfomatics
Needleman-Wunsch algorithm. Use matrices, as described in lecture, to identify matches/mismatches to find the best alignment. Show your work: submit both the matrices you used and the final “best” alignment(s) in order to receive full credit. Use 1 for match, 0 for mismatch, and 0 for gap penalty.
RSGEW and RTFGE
FKYAVIR and DKYVIRGN
Suggestion: use a spreadsheet program, such as Excel, to create the similarity matrices. Then, copy the matrices in a text editor, such as
Word, to submit your assignment, together with the rest of the write-up.
Solve Problems/Computer Lab questions 4.7 (Pol protein in HIV) and 4.9 (E value), Pevsner page 161.
Solve Problems/Computer Lab question 9-3 (frequency of variants HBB vs HLA) Pevsner page 424.
This assignment is worth 40 points.
