7 replies to this topic

[jen_23]

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

[DELETEMYACCOUNTPLEASE]

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

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

go here: http://www.expasy.ch/tools/blast/
enter your sequence
click "Run BLAST"
wait.

Where are you doing your masters degree and what in?

[DELETEMYACCOUNTPLEASE]

If you want to do PSI-BLAST:
http://blast.ncbi.nl...K_LOC=blasthome

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

[pito]

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

If you want to do PSI-BLAST:
http://blast.ncbi.nl...K_LOC=blasthome

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

Cant you just select the PSI-BLAST (Position-Specific Iterated BLAST) Algorithm (the second option) ?

Or do you always need to do 2 blasts?

[DELETEMYACCOUNTPLEASE]

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

[pito]

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)

[DELETEMYACCOUNTPLEASE]

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.

[pito]

Ah I see.