Some Bioinformatics/Biology related little programs for fun/laziness
A program that uses Needleman–Wunsch algorithm to do sequence global alignment and local alignment with dynamic programming (dp)
Extending on the sequence alignment project. Build phylogenetic tree from amino acid sequences of hemogloblin subunit alpha-a. Build evolutionary tree of cat, human, chicken, macaw, 2 macaque speices using blosum62 matrix. Compared and contrast 2 trees build by UPGMA algorithm and by brute force parsimony tree finding (using Sankoff Dynamic Programming to calculate parsimony score).
(work with Bowties' output, xxx_coverage.txt)
For my Bioinformatics class at Carleton College with amazing prof Rika Anderson, the prokka annotation in our server is always named by a machined code, such as "KGOCCMOE_00001" (from projects with Tara Dataset). These machine codes assure a variety of programs, such as Bowtie2, run smoothly, but if there is no way you will that know "KGOCCMOE_00001" is actually "Argininosuccinate synthase" (much more interesting)? If you want to do that, put xxxx_coverage.txt and xxxx_ORFs.faa in the same folder as this script, direct to that folder in your terminal and run: python merge_name.py [ORF_coverage.txt] [ORFs.faa] And there is a file with human readable names, as well as the relative abundance of that corresponding gene!