Sequence Alignment Scripts for Intro to Bioinformatics Course

Open Courseware to demonstrate usage of sequence alignment tools using Unix Bash Shell and BioPython.

Covers pairwise sequence alignment, BLAST, multiple sequence alignment, and Hidden Markov Models.

Bash Shell scripts to install BLAST, CLUSTALW, MUSCLE, T-COFFEE, and HMMER.

BioPython scripts run sequence alignment on HIV gag-related proteins, including human Arc protein.

Arc alignment example inspired by this paper from Cell:

Pastuzyn, E.D., Day, C.E., Kearns, R.B., Kyrke-Smith, M., Taibi, A. V., McCormick, J., Yoder, N., Belnap, D.M., Erlendsson, S., Morado, D.R., Briggs, J.A.G., Feschotte, C., Shepherd, J.D. The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer. Cell 172, 275–288.e18 (2018).