Date of Award

Spring 2012

Document Type



Mathematics, Engineering & Computer Science


Using a created a program in MatLab, several amino acid sequences can be aligned with one another so they can be examined for biological significance. Sequence alignments are used to determine similarities in proteins and from this information, make inferences on protein functionality. The program accomplishes this by setting a cost for gaps in a sequence or substitution of one amino acid for another. A dynamic programming algorithm called the Needleman & Wunsch Algorithm is used to find several possible global pairwise alignments. These pairwise alignments are used to form a multiple sequence alignment, which compares a number of like sequences together to look for highly conserved, and therefore possibly biologically important, sections.