Biopython Help

[asf33]

I am studying protein-protein interactions between the AR(fl) and its coactivators. The AR-NTD and AR-CTD homodimerize, and coactivators seem to also bind to the CTD, potentially in the region that AR-NTD binds. Therefore, I am trying to write a script to make it easy for me to align the sequences of AR-NTD and certain coactivators. However, I am very new to biopython, and to writing scripts. Would anyone be able to help me to write a script to download protein sequences from NCBI, align the sequences and produce a consensus sequence? I ultimately want the script to print the consensus sequence at the end. I'm also not very familiar with "clustal", but after talking to a friend, they had mentioned it could be useful. Thank you for any and all advice.

[maubp]

The NCBI Entrez utilities could be used via Biopython to search for and download protein sequences via Biopython - although depending on the numbers it might be simpler to manually select proteins of interest? How many proteins are you looking for? e.g. A dozen, or a hundred?

Aligning the sequences could be done with a tool like Clustal Omega or MUSCLE - both of which you can call from Biopython, but for one or two alignments there is little point compared to running the tool by hand.

Once you have an alignment, getting the consensus is possible with Biopython - or indeed many alignment tools (e.g. Jalview). Again, if you are only doing this once or twice I see little reason to automate it via Biopython.