https://github.com/jananiravi/2020-molevol-phylogeny

Supporting material for the "Molecular Evolution and Phylogeny" lecture | Feb 27, 2020
https://github.com/jananiravi/2020-molevol-phylogeny

computational-biology michigan-state-university molecular-evolution phylogeny

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Supporting material for the "Molecular Evolution and Phylogeny" lecture | Feb 27, 2020

• Host: GitHub
• URL: https://github.com/jananiravi/2020-molevol-phylogeny
• Owner: jananiravi
• License: mit
• Created: 2020-02-25T17:27:03.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2020-02-27T02:11:14.000Z (almost 5 years ago)
• Last Synced: 2024-03-20T10:20:41.461Z (10 months ago)
• Topics: computational-biology, michigan-state-university, molecular-evolution, phylogeny
• Size: 2.94 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Molecular Evolution and Phylogeny

Supporting material for the Feb 27, 2020 lecture in the ['Chemistry & Biology of Pathogens' special seminar course](https://d2l.msu.edu/d2l/home/992472)!

## Learning Objectives

- Intro to computational evolutionary biology

  - Molecular Evolution & Phylogeny

  - Comparative Pathogenomics

- In class hands-on demo for two most useful tools: [BLAST](https://github.com/jananiravi/2020-molevol-phylogeny#blast) & [Interproscan](https://github.com/jananiravi/2020-molevol-phylogeny#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](https://github.com/jananiravi/2020-molevol-phylogeny/tree/master/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](https://www.ebi.ac.uk/interpro/result/InterProScan/iprscan5-R20200227-014609-0200-91060680-p1m/)

  - [Interpreting InterProScan results](https://www.ebi.ac.uk/interpro/help/tutorial/)

- **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](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=5E7UXJ5101R)

  - [Interpreting BLAST results](https://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_BLAST_NewResultPage.pdf)

- **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]