Day 1
Homology, Alignments & Phylogeny

Material

• Slides

• Notebook - Parsing and filtering MSA

• Notebook - Introduction to JAX

• Optional - Notebook - Phylogeny (we'll use SeaView)

• Optional - Notebook - UPJMA/NJ in numpy

Databases

• Uniprot - The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

Servers/Software

• Multiple sequence alignment generators

  • BLAST - (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

  • Jackhmmer - iterative search vs protein sequence database, using profile hidden Markov Models

  • HHblits - 'lightning-fast' HMM-HMM-based iterative sequence search tool

• Seaview -  is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. 

• Weblogo -  A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment.

Python libraries

• biopython - Python Tools for Computational Molecular Biology