mfileman / dna-motif-search Goto Github PK

This was a project for my bioinformatics class. We studied a couple of motif finding algorithms for finding a potential motif in n many randomly generated DNA sequences. This project 1) randomly generates n many DNA sequences 2) randomly generates a kmer 3) edits up to d many positions in that kmer & inserts that kmer (now motif) into each sequence From here, 4) blindly reads these sequences (with emplaced motifs) and 5) brute force searches all n sequences to find n many motifs with the lowest hamming distance from a consensus string 6) Utilizes Gibbs Sampling algorithm (a randomized algorithm) to find the lowest overall hamming distance from a motif profile Implemented in Swift.