Protein and DNA Sequence alignment: finding and comparing sequences

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Authors: Susan Coort, Chris Evelo, Egon Willighagen, Lars Eijssen, Friederike Ehrhart

Protein and DNA Sequence alignment: finding and comparing sequences is an Open Educational Resource (OER) for first year biomedical sciences students into the world of sequence alignment and BLAST.

Table of Contents

1. Introduction
     1.1 From DNA via RNA to proteins
       1.1.1 Codons
       1.1.2 Protein folds
       1.1.3 Similar sequences
     1.2 Examples of sequence comparison
       1.2.1 Comparing DNA sequences
       1.2.2 Comparing RNA sequences
       1.2.3 Comparing protein sequences
   
2. Comparing sequences
     2.1 Comparing protein or nucleotide sequences?
3. Aligning two short DNA sequences
     3.1 Gap
     3.2 Scoring Matrices
4. Aligning protein sequences
     4.1 Substition matrices: PAM and BLOSUM
       4.1.1 PAM matrices
       4.1.2 BLOSUM matrices
5. Which BLAST to use
   
6. Interpreting BLAST output
     6.1 Max and Total scores
7. The FASTA format
   

Educational material

Video's by National Center for Biotechnology Information (NCBI):

• NCBI Minute: A Beginner's Guide to Genes and Sequences at NCBI (time: 33:43 min)
• Webinar: A Practical Guide to NCBI BLAST (54:44)
• BLAST Results: Expect Values, Part 1 (2:29)
• BLAST Results: Expect Values, Part 2 (3:39)
• NCBI Minute: Five Teaching Examples Using BLAST (29:37) (booklet)
• NCBI Minute: Using BLAST Well (45:53)

Additional resources can be found in the ELIXIR Training Portal TeSS.

Literature

• Mount DW. Using the Basic Local Alignment Search Tool (BLAST). Cold Spring Harb Protoc. 2007 Jul;2007(7):pdb.top17. doi:10.1101/PDB.TOP17
• Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences. 1992 Nov 15;89(22):10915–9. doi:10.1073/pnas.89.22.10915
• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology. 1990 Oct;215(3):403–410. doi:10.1016/S0022-2836(05)80360-2

License

CC-BY 4.0 International Authors, source code.