Blasts and MSAs - (Mar/20/2010 )

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

Thanks

jen_23 on Mar 20 2010, 02:15 PM said:

If you want to do PSI-BLAST:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PR...K_LOC=blasthome

The first time you run it you only get BLAST results. Run it again and you are entering PSI-BLAST.

perlmunky on Mar 21 2010, 08:11 PM said:

I don't think it does another iteration unless you click a button. I tend to use command line tools rather than web stuff.

But I would think that if you select the PSI-BLAST Algorithm and then push blast, it would automatically use the PSI-BLAST.

It does seem strange you need to run it twice.

Oh well, I dont really use it, it was just something that seemed strange to me.

Command line tools? What do you mean with that?
I am only used to use webstuff like ncbi (not the protein blast tough)

I checked. I took a sequence from the pdb (3chy) and used the psi-blast option. Clicking once runs a single iteration of psi-blast, to do another iteration you must click "go". By command line, I mean I have a local copy of blast (from NCBI-TOOLS) and a copy of the NR databases against which I create MSAs.

I seemed strange to me too ... it does however offer the user full control, in addition to confusing students.

Ah I see.