README.md

Molecular Evolution and Phylogeny

Supporting material for the Feb 27, 2020 lecture in the 'Chemistry & Biology of Pathogens' special seminar course!

Learning Objectives

• Intro to computational evolutionary biology
  • Molecular Evolution & Phylogeny
  • Comparative Pathogenomics
• In class hands-on demo for two most useful tools: BLAST & Interproscan
  • For this, please explore the tools below | web-versions for the 'how' + papers to orient you on the 'why' & 'what'
  • Example input files in the data folder: fasta + saved BLAST search strategy.
  • We will address your Qs + use these with the web-tools in class on Thursday!

Interproscan

• The tool: https://www.ebi.ac.uk/interpro/search/sequence/
  • Example run
  • Interpreting InterProScan results
• Papers:
  InterProScan 5: genome-scale protein function classification. Jones et al., Bioinformatics. 2014 May 1;30(9):1236-40. doi: 10.1093/bioinformatics/btu031. https://www.ncbi.nlm.nih.gov/pubmed/24451626
  InterPro in 2017-beyond protein family and domain annotations. Finn et al., Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. https://www.ncbi.nlm.nih.gov/pubmed/27899635
• Wiki: https://en.wikipedia.org/wiki/InterPro

BLAST

• All BLAST Tools: https://blast.ncbi.nlm.nih.gov/Blast.cgi
  • Example run
  • Interpreting BLAST results
• Protein BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins
• Original paper (harder to read):
  Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. J Mol Biol. 1990 Oct 5;215(3):403-10. https://www.ncbi.nlm.nih.gov/pubmed/2231712.
• Easier to read paper:
  Steps Used by the BLAST Algorithm. Mount DW. CSH Protoc. 2007 Jul 1;2007:pdb.ip41. doi: 10.1101/pdb.ip41. https://www.ncbi.nlm.nih.gov/pubmed/21357114
• Wiki: https://en.wikipedia.org/wiki/BLAST_(biotechnology)

Questions?

[email protected]