Dynamic Programming in Bioinformatics: Global Alignment with Needleman-Wunch Algorithm - P, Assignments of Biology

Download Dynamic Programming in Bioinformatics: Global Alignment with Needleman-Wunch Algorithm - P and more Assignments Biology in PDF only on Docsity! Homework 2---- Bioinformatics 1 Fall 2005 Write a pseudocode program to do "dynamic programming." The result should be a global alignment of two sequences, with a linear gap penalty (Needleman-Wunch algorithm). Do the program in three parts: (1) Forward summation. Use the variable name Mat (i.e. Mat[i,j] for the forward sum values at position i (in seq1) and j (in seq2)) and use the variable name Trace (i.e. Trace[i,j]) for the Traceback setting. Use traceback symbols as in the notes (they are just symbols and have no numerical meaning) (2) Traceback. Start at the end and save the series of traceback symbols until you reach the begining (0,0). Then reverse the order of traceback symbols. Save the result in the variable array Tb (i.e. Tb[i]) (3) Translate the traceback (Tb) into an alignment. Write out the first sequence with gaps, one character at a time (write either seq[i] or “~”). Then write out the second sequence with gaps. Use pseudocode. Due Monday 9/19