Searching for protein motifs with MEME I am trying to look for motifs in a set of proteins returned by a mass spec experiment using MEME. The experiment was carried out in the yeast Candida albicans.

Does anyone know if it is worth calculating either a custom background model or a position specific prior using the non-hit proteins? I don't generally bother for nucleotide motif searching, but I've never done protein motif searching before. 

Also advice of whether to use the ZOOPS or ANR models appreciated: is there any reason not to use ANR other than run time?
Some answers by the author Charles Grant via the MEME Suite Google group may be useful to you.

Via: https://groups.google.com/forum/#!topic/meme-suite/yNascbE8Tig/discussion


  Providing your own higher-order background model can greatly improve MEME's ability to discover motifs...
  
  The command-line utility fasta-get-markov, included in the MEME Suite download, is used to generate custom background Markov models. The input to fasta-get-markov is a FASTA file containing "background" sequences. Ideally, these "background" sequences will be different from the sequences you are analyzing with MEME, but as similar in nature as possible. For example, if you wanted to discover motifs in certain intergenic regions, you might use other sequence data from other intergenic regions to generate the background. The larger the set of "background" sequences is, the better the results will be...
  
  Typically, you should not specify an order larger than 3 for DNA sequences, or larger than 2 for protein sequences. However, if your input sequences contain higher-order non-random effects that are getting in the way of motif finding, you can follow the following "rules of thumb":
  
  
  Use a background model at least four orders less than the shortest motifs you are looking for. So, if you want to find motifs as short as six, I wouldn't use a model higher than order two. 
  For an accurate model of order N, you need to use a FASTA file as input to fasta-get-markov with at least 10 times 4**(N+1) DNA characters in it. 
  
  
  So,
  
  
  order-3 requires 2560 characters 
  order 4 requires 10240 characters 
  order 5 requires 40960 characters etc.
  


I'm not certain if that input requirement scales differently for proteins (i.e., 20^(N+1)). That may be worth following up on the Google group.

And via: https://groups.google.com/forum/#!topic/meme-suite/UiDhdY6WlK4/discussion


  You should choose the motif occurrence model based on your understanding of the experimental protocol that generated the sequence data and the underlying biology. MEME is trying to find short sequences that are statistically over-represented in your sequence data. To do this, it has to assume a model for how many occurrences of a motif there will be in each sequence. The nature of your experiment should be the basis for the model you choose. For example, data from a ChIP-Seq experiment will typically contain exactly one occurrence of a motif per sequence. On the other hand, sequences drawn from a database of upstream regions of co-regulated genes might contain any number of motif occurrences, including 0.


Via: https://groups.google.com/d/topic/meme-suite/QJiJsy1QxYk/discussion


  The MEME algorithm run time is cubic with respect to the number of input sequences, therefore, it is unsuitable for OOPS (only one per sequence) analyses that have more than 1000 sequences. For ZOOPS (zero or one per sequence) and ANR (any number of repeats) analyses, having more than 1000 sites are also intractable in terms of run time. For example, on a 3 GHz CPU, initialization of the p-value table takes about 10 min for 1000 sites/sequences in OOPS, about a day for 5000 sites, and about 1 week for 10,000 sites. Then the quadratic run time with respect to the total number of characters kicks in next.


Thus it seems like the ZOOPS and ANR models have similar runtime complexity, and use of the MPI-based parallel meme_p binary may be helpful, depending on your analysis:


  The parallel version of MEME scales up to about 128 processors. Please see http://www.sdsc.edu/~tbailey/papers/cabios96.pdf for a discussion of the parallel program. You must bear in mind however, that doubling the total number of sequences input to MEME means that you will need 8 times more processors for the job to finish in the same amount of time.