Bioinformatics Algorithims
Algorithms being implemented are Quicksort, Needleman-Wunsch, K-means clustering, PSSM, and a Gibbs Sampler
Files for sorting are: sample100k.fastq sample10k.fastq sample1k.fastq //sorting based upong sequence
g++ try.cpp && time ./a.out sample1m.fastq > test.txt
Files to be aligned: RpoB-B.subtilis.fasta RpoB-E.coli.fasta //Run Needleman_Wunsch Alignment with match score, mismatch score, and gap score
g++ jack_NW.cpp -o ts ./ts RpoB-B.subtilis.fasta RpoB-E.coli.fasta 1 -3 -4
File to be clustered bacteria.txt //K means clustering algorithm with ranging centroid possibilites from min to max number
g++ Jack_Clustering.cpp -o cls ./cls bacteria.txt 3 7
Files to have PSSM ran on are FurR.txt and ecoK12-MG1655.fasta //PSSM algorithm with minimum scores shown
g++ ustanik_pssm.cpp -o ps ./ps FruR.txt ecoK12-MG1655.fasta 15
Files to have Gibbs sampler ran on are E.coliRpoN-sequences-16-100nt.fasta E.coliRpoN-sequences-6-300nt.fasta //Gibbs sampler program with listed initial start size
g++ ustanik_gibbs.cpp -o gb ./gb E.coliRpoN-sequences-16-100nt.fasta 39