software to look for aminoacid motifs after a MEME analysis of a PSI-Blast run

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Article #2535

#2535

From: Gabriele Zoppoli
Date: Sun, 16 Jan 2011 14:15

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Dear Mailing List,

I retrieved with PSI-Blast the top 100 proteins with similarity to the one
I'm interested in.

I then ran the 100 FASTA protein sequences into MEME, to find conserved
motifs across these proteins.

I retrieved a list of "candidate" motifs which are highly conserved across
the vast majority of my input.

I would now like to know if any of these candidate motifs corresponds to
something already described in databases and/or literature, through freeware
software that allows me to input the conserved aminoacid motifs I discoved
with MEME and compare them with known ones.

Where should I look at? What shall I do?

Thank you all in advance

Gabriele Zoppoli

-- 
“So what’s getting ubiquitous and cheap? Data. And what is complementary to
data? Analysis. So my recommendation is to take lots of courses about how to

manipulate and analyze data: databases, machine learning, econometrics,
statistics, visualization, and so on.” Professor Hugh Varian, Chief
Economist at Google, speaking to the New York Times in February 2009.

"In God we trust, all others bring data." William E. Demings (1900-1993)

**"Prediction is very difficult**,especially** about the* future"*. Niels
Bohr (1885 - 1962)

"How can I help seeing what's in front of my eyes? Two and two are four".
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Sometimes they are all of them at once". George Orwell, *1984*.

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Date: Sun, 16 Jan 2011 15:15:29 +0100
From: Gabriele Zoppoli <zoppoli@gmail.com>
To: bio-soft@magpie.bio.indiana.edu
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subject: software to look for aminoacid motifs after a MEME analysis of a
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