Exploring computational biology while learning Java. Projects include: -- Open Reading Frame Finding ("ORF_Finder") -- Pairwise/Multiple Alignment (through dynamic programming in "Alignment") -- Gene Finder (through Hidden Markov Models. The states include: Introns, Intergenic States, Codons, StopCodons, StartCodons) -- Genome Assembly (through de Bruijn Graphs) and Sequence Mapping (through Burrows-Wheeler Transform) -- RNA Secondary Structure Prediction from RNA sequence & RNA Hybridization (using Viterbi Algorithm) -- Gene Clustering (trying different methods: K-means & hierarchical & CAST clustering) -- Gibbs & EM Motif Search in sequences
This project is a work in progress.