List of Java Programs

Partial list of programs done by me as freelance or as part of various courses.

  • Bioinformatics Programs

    Done as part of the courses taken at UW-Madison. Programs are available on request (so that students don't copy readily from here).
    • Implementation of Dynamic Programming for computing pairwise local sequence alignment.
    • Hidden Markov Model for gene finding.
    • Neighbor-joining algorithm for inferring phylogenetic trees.
    • The k-means clustering algorithm and apply it to a small gene-expression data set.
    • Pairs-HMM based algorithm to find the most accurate local alignment.
    • ZOOPS version of MEME for Motif Finding combined with the Random projection method for picking seeds.
    • Jukes-Cantor model of evolution with specified "alpha" parameter that uses ML-distance to compute a nearly optimal probabilistic phylogenetic tree. Compute the likelihood using Felsenstein's algorithm.

  • J2ME Programming: Java Mobile Edition

    I took up a project in the department of Botany at UW Madison. Though the project writeup was for database programming, the definition expanded to incude a GUI design for the sampling and surveying of the vegetation (trees and herbs) for Wisconsin forests. It was a interesting project, and I had to follow a steep learning curve into the world of J2ME programming. I had to program for Palm OS, which was also new to me.
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