Multiple sequence alignment to find conserved regions

Question

[fabbrl]

Hi all! I am doing homology modeling for a transmembrane protein (sodium channel). I am still in the phase of aligning the sequences (query and template(s)). To better determine the sub-cellular location of the different segments and to improve the quality of the alignment, I have to do a multiple sequence alignment. My advisor was very vague and I am new to all of this. I saw that in many different studies this is a common thing to do (many papers with the picture of the MSA highlighting the conserved regions etc...). Nevertheless, I found no tutorial explaining how to do this. I only know that I need many sequences that I should then align to find the conserved regions. How do I find all these sequences? Can I use Blast? At the moment I used it to find my template (homologous) using PDB in the option (since I need a structure). Is it a good idea to find the sequences of the members of the sodium channel family (SCNxA, x = 1:11) of human and other species and then align them? Do I have to bother myself with the value of identity or not for this phase?

Thanks a lot.

Answer 1

[natasha.sernova]

There are many tools that can do it. Try some of them and select the most sutable for sodium channels:

https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml

WIKI gives a software overview:

https://en.wikipedia.org/wiki/Multiple_sequence_alignment#Motif_finding

There is a nice collection of tools to look at:

http://geneinfinity.org/sp/sp_alignments.html#multiple

[fabbrl]

Thank! I'll have a look.

Answer 2

[Elisabeth Gasteiger]

You may want to have a look at the video tutorials on how to use BLAST and Align on the UniProt website:

BLAST:

Align (uses ClustalO):

In particular, UniProt's Align interface allows you to highlight similar regions and annotated features in different colours. Please don't hesitate to contact the UniProt helpdesk if you have any specific questions about these services.