Blasts and MSA

jen_23 wrote: »

So can anyone tell me how to easily blast a protein sequence and perform multiple sequence alignments using the web based tools such as found on expasy?

I'm having a serious brain malfunction here. I'm pretty sure I did this at the start of my masters no problem now at the end it's gone :rolleyes:

Thanks

Hi Jen

Performing blast's via ExPASy is fairly straightforward;
go to ExPASy homepage, and click on 'blast' link (under tools and software); it is automatically set up to do a blast-P - protein seq blast. Enter your seq, hit enter and voila.

Performing MSA's using ExPASy is not something i am familiar with, will give you an alternative;

once you have your seq's, go to clustalw homepage; enter each seq as folows:

> seq1

> seq2

> seq3

etc

The > symbol is important here; without it the software wont read your seq's properly.

So enter your protein seq's as above, and then perform the MSA.

If you need any further help, feel free to pm.

Hope the above helps