Conduct a MetaMEME search

4. Return to the MEME output document in the browser, and click on the MetaMEME button. Fill in the form shown in Figure 2.4.22. Use the Browse button to enter the name of the training set used with MEME. Then, select the Yeast database to search. Next, click on Submit. Click on Submit in the next form that appears to accept the search defaults. MetaMEME will perform its search and return a hidden Markov model, a multiple alignment of the training set, and search results on the chosen sequence database.

Several other databases are available for searching, including SwissPROT and the NCBI nonredundant (nr) database.

Other options are available to MetaMEME users, but are beyond the scope of this protocol. See http://metameme.sdsc.edu for more information on MetaMEME.

5. Click on Database Search Results on the MetaMEME form to see the Yeast sequences that match the model of the bacterial protein family built by MetaMEME (Fig. 2.4.23).

The two top hits are the same ones as detected by MAST.

From Current Protocols in Bioinformatics Online Copyright © 2002 John Wiley & Sons, Inc. All rights reserved.

CURRENT PROTOCOLS IN BIOINFORMATICS CHAPTER 2 RECOGNIZING FUNCTIONAL DOMAINS UNIT 2.4 Discovering Novel Sequence Motifs with MEME

ALTERNATE PROTOCOL 1: FINDING REPEATED MOTIFS IN PROTEIN SEQUENCES

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