How Do I Cause A Psi-Blast Alignment To Iterate?

Question

[Doug]

How do I cause a Psi-Blast alignment to iterate? I've checked the documentation and I understand that the way it works is to do multiple iterations of profile generation and alignment. However, when I perform a search it seems to only do one iteration and I cannot find where to ask it to move to the next iteration.

Answer 1

[Doug]

Apparently on the results page, under the graphic display of the multiple sequence alignments, and under the Descriptions heading, there is a "Legend for links to other resources" followed by a not very noticeable line of text that reads "Run PSI-Blast iteration 2 with max [500]" followed by a "Go" button. This is what is used to move to the next iteration of PSI-Blast.

Note that documentation in several places says that there is a "Run Psi-Blast Iteration" button, but there is no such button that I can see. Instead there is only that text followed by a "Go" button.

[Michael Schubert]

On the web interface this has got a reason: you can thus choose on which sequences you want to build your profile on, not just take any similar ones.