HW1 - Online Exercise and Basic GitHub Usage

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A. Online Excercise: Databases and Software Tools

This is an easy warm-up homework exposing students to a variety of online databases and software tools. This exercise will be used to create a result file, that will be uploaded to each participant’s private GitHub homework repository. Apart from exposing students to some useful web services, it serves mainly as an exercise to get familiar with GitHub by uploading the final result file (here PDF) to each student’s private homework repos on GitHub.

1. Go to http://www.ncbi.nlm.nih.gov, select Protein database in dropdown, and then run query: P450 & hydroxylase & human [organism], select under Source databases UniProtKB/Swiss-Prot
   1. Report final query syntax from Search Details field.

2. Save GIs of the final query result to a file. For this select under Send to dropdown GI List format.
   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

6. BLASTP against the PDB database (use again first P450 in your list).
   • On result page select first entry in BLAST hit list (here 3K9V_A)
   • Select ‘Protein 3D Structure’
   • If you see multiple results on the subsequent page, choose one of them (e.g. the first one).
   • Select option “full-featured 3D viewer” in the bottom right corner of the structure image
   • Choose the ‘Details’ tab on the right. After this the structure of the protein is shown on the left and the underlying protein sequence on the right
   • Highlight the heme binding cysteine in the structure by selecting it in the sequence
   • Save the structure view to a PNG/JPG image file or take a screenshot

B. Homework Submission to a Private GitHub Repository

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 homework will be due one week after they are assigned. This one is due on Thu, April 10th at 6:00 PM.

Homework solution

A solution for this homework is not required since the tasks are identical to the steps described above under sections HW1A-B.