motif search tool for my alignment

Emir Khatipov ekhatipo at NOSPAMmidway.uchicago.edu
Sat Mar 17 18:05:11 EST 2001


Does anybody know (a) (web)tool(s) that would take a number of pre-aligned
(short) sequences at once and output a consensus motif, as well as would
point out similarity to known functional motifs?

For example, submit:

actyrcll
ictwkcml
vcyyhcwv
...

and get as a result something like:

[hydrophobic]-cysteine-[hydroxyl]-[aromatic]-[positive]-cysteine-[hydrophobi
c]-[hydrophobic]
similar to, e.g., phenyl-binding motif

Thank you for pointers.

Emir





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