HW1 - Online Exercise and Basic GitHub Usage
3 minute read
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.
- 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- Report final query syntax from Search Details field.
- Save GIs of the final query result to a file. For this select under
Send to
dropdownGI List
format.- Report the number of retrieved GIs.
- Retrieve the corresponding sequences through Batch-Entrez using GI list file as query input -> save sequences in FASTA format
- Generate multiple alignment and tree of these sequences using MultAalin
- Save multiple alignment and tree to file
- Identify putative heme binding cysteine in multiple alignment
- Open corresponding UniProt page and search for first P450 sequence in your list.
- Compare putative heme binding cysteine with consensus pattern from Prosite database (Syntax)
- Report corresponding Pfam ID
- BLASTP against PDF database (use again first P450 in your list);
on result page click first entry in BLAST hit list (here 3K9V_A); then select ‘Identify Conserved Domains’ on side bar; click grey bar labelled ‘CYP24A1’; then select ‘Interactive View’ under ‘Structure’ menu which will download a file named ‘pfam00067.cn3’.
- Compare resulting alignment with result from MultAlin
- View 3D structure (pfam00067.cn3) in Cn3D*, save structure (screen shot) and highlight heme binding cysteine. Note, Cn3D* can be downloaded from here.
*If there are problems in the last step (6.2) with the install of Cn3D, then please use this online only alternative: (i) click in the 3K9V_A page ‘Protein 3D Structure’ instead of ‘Identify Conserved Domains’; (ii) choose one of the two structure entries provided on the subsequent page; (iii) select option “full-featured 3D viewer” in the bottom right corner of the structure image; (iv) choose the ‘Details’ tab on the right; (v) after this the structure of the protein is shown on the left and the underlying protein sequence on the right; (vi) highlight the heme binding cysteine in the structure by selecting it in the sequence; and (vii) then save the structure view to a PNG 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 13th at 6:00 PM. You have unlimited attempts. Students can edit and re-upload files anytime before the deadline.
Homework solution
A solution for this homework is not required since the tasks are identical to the steps described above under sections HW1A-B.