Computational Exploration of Protein Function Mentor

[studentneedshelp]

Hi

I've started this project and I've done a lot of research on the subject. I believe I understand the concepts but I'm having a little trouble with using the websites. For instance, I started with with AAMP, found human mRNA and amino acid sequences, and used BLAST to find mRNA and amino acid sequences for rats, orangutans, and cows. But what is the next step? I know it is to create a multiple sequence alignment, but how do I do that? Please help!

Thank you

[deleted-70091]

Hi. I have read a little bit about the computational exploration of protein function project. I think you need to use one of the websites provided on the page (found here:https://www.sciencebuddies.org/science- ... p002.shtml).

This is one of the websites: http://tcoffee.vital-it.ch/cgi-bin/Tcof ... /index.cgi

Have you tried this?

[studentneedshelp]

Hi,

so T-Coffee didn't work but ClustalW2 did. But I decided to change my gene of interest to CFTR and did a multiple sequence alignment for 16 different species. But on step 5 it says to input your amino acid sequence into a domain database. Do you just put one of the amino acid sequences, for instance, the homo sapien one for CFTR into the website and look for the domains or all of them individually? And when looking at the multiple sequence alignment, how do you determine the conserved region?

Thank you

[mbadtke]

student,
Did you resolve your issues with ClustalW? I have used the program before, if you are still not sure how to proceed I can try to walk you through it. Here are some FAQs that might help you.

http://www.ebi.ac.uk/Tools/msa/clustalw2/help/faq.html

Matt Badtke