Two Questions for the Bioinformatics


Oct 1, 2013 (3 years and 8 months ago)


Two Questions for the Bioinformatics

home Mid
term Exam, 2005.

1. (Lifted from 547; a ``theoretical” question.)
overlapping matches.

Write an
algorithm which follows up on the Smith
Waterman algorithm, and finds the best local
match of two seq
uences which doesn't overlap the best local match already found. Repeat
this as well. Why would this be useful for protein sequences? “Write an algorithm” can
mean writing pseudo
code for such. You do not have to write code for this.

This algorithm is som
etimes referred to as the Waterman
Eggert algorithm. If you use the
literature, be sure to cite it.

PAM Matrices.
What kind of data was used to construct the PAM(1) matrix? What
does it mean to say that the other PAM matrices were derived from PAM(1)
by a time
independent Markov process?