Topic: Databases and Software

This is an easy warm-up homework exposing students to a variety of online databases and software tools.

  1. Go to http://www.ncbi.nlm.nih.gov, select protein DB, run query: P450 & hydroxylase & human [organism], select under Source databases UniProtKB/Swiss-Prot

    1. Report final query syntax from Details page.
  2. Save GIs from this final query to file (select GI List format under display)
    1. Report the number of retrieved GIs.

  3. Retrieve the corresponding sequences through Batch-Entrez using GI list file as query input -> save sequences in FASTA format

  4. Generate multiple alignment and tree of these sequences using MultAalin

    1. Save multiple alignment and tree to file
    2. Identify putative heme binding cysteine in multiple alignment

  5. Open corresponding UniProt page and search for first P450 sequence in your list.

    1. Compare putative heme binding cysteine with consensus pattern from Prosite database (Syntax)
    2. Report corresponding Pfam ID
    3. How many mouse (Mus musculus) sequences are in this family (use species tree from Pfam db)
  6. BLASTP against nr database (use again first P450 in your list); on next two pages click on P450 and CypX domains, respectively (this runs RPS-BLAST).
    1. Compare resulting alignment with result from MultAlin
    2. View 3D structure in Cn3D, save structure (screen shot) and highlight heme binding cysteine

Homework submission

Please assemble the results of this homework in one PDF file and upload it to your private course GitHub repository under Homework/HW1/HW1.pdf.

Due date

Most homeworks will be due one week after they are assigned. This one is due on Thu, April 12th at 6:00 PM.