Principles and Applications of Modern DNA Sequencing

EEEB GU4055

Session 5: Phylogenetics I

Notebook 4.1: OrthoDB

Notebook 4.2: BLAST, NCBI, and APIs

BLAST is an algorithm for comparing sequences, it searches the NCBI database. The NCBI Entrez tools provide an API interface to this database. These tools have facilitated the development of complex tools like OrthoDB.

Notebook 4.2: Requests to query APIs


  import requests

  # search term
  term = "FOXP2[GENE] AND Mammalia[ORGN] AND phylogenetic study[PROP]"

  # make a request to esearch 
  res = requests.get(
      url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi", 
      params={
          "db": "nucleotide",
          "term": term,
          "sort": "Organism Name",
          "retmode": "text",
          "retmax": "20",
          "tool": "genomics-course", 
          "email": "de2356@columbia.edu",
          },
      )
        

Notebook 4.2: Requests to query APIs


  # returns a response object
  res = requests.get(...)

  # the URL is built from the params arguments to requests.get()
  res.url
        

  'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=FOXP2%5BGENE%5D+AND+Mammalia%5BORGN%5D+AND+phylogenetic+study%5BPROP%5D&sort=Organism+Name&retmode=text&retmax=20&tool=genomics-course&email=de2356%40columbia.edu'
        

Notebook 4.2: Requests to query APIs


  # returns a response object
  res = requests.get(...)

  # the text attribute store the returned HTML
  res.text
        

 
        

Phylogenetics I

A practical guide to inferring phylogenetic trees.