Description
Kelleybioinfo.org is an interactive bioinformatics software that was built by Dr. Scott Kelley's team in 2013 that teaches basic theories in bioinformatics in BIOMI 563 class at San Diego State University (SDSU). Equipped with five modules with two algorithms in each module, it offers 10 interactive bioinformatics learning platform. Kelleybioinfo software is also accessible through web browsers, handheld devices, or tablets. The National Science Foundation (NSF) has recently awarded a grant for a further development of this software and therefore we will introduce and develop the scoring matrix module. The scoring matrix module offers the basic concept of point accepted mutation (PAM) and block substitution matrix (BLOSUM). Scoring matrices such as PAM, BLOSUM, or Gonnett matrix have been widely used to score matches, mismatches, substitutions, and deletions in sequence alignments. This module will simulate global (for PAM) or local (for BLOSUM) protein sequence alignment and to determine protein's mutability based off the log-odd matrix. There has not been a single interactive tutorial on how PAM's or BLOSUM log-odd matrix are generated. Therefore having this module in kelleybioinfo.org will help students who learn bioinformatics to understand the PAM or BLOSUM matrix's concept.
