Intro to Sequence Similarity Searching for Public Health Bioinformatics

By: Joel Sevinsky

June 14, 2020

The webinar is from Session 8 of the June 2020 AMD Acadmey. It is hosted as an unlisted video and no password is required. The slides for this presentation can be found HERE.

Additional resources

There were many references discussed in this presentation. Most of those references can be found in this Paperpile library.

During the ANI-MASH portion, there were several Tableau visualizations. These visualizations are linked in my original ANI-MASH presentation HERE.

Some additonal BLAST links are:

The following videos are an excellent description of the BLAST algorithm presented by Dr. Rob Edwards at SDSU. The videos are highly recommend to the student to get a better understanding of the algorithm, its history, and applications beyond just DNA:DNA pairwise comparions.

  1. BLAST 1
  2. BLAST 2 seed and extend
  3. BLAST 3 amino acid differences
  4. BLAST 4 PAM vs BLOSUM
  5. BLAST 5 BLOSUM62
  6. BLAST 6 scoring alignments
  7. BLAST 7 scoring gaps
  8. BLAST 8 Probability
  9. BLAST 9 E values
  10. BLAST 10 Algorithms
  11. BLAST 11 PSWM