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.
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.
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.
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