Advanced options

In the course of building and using a motif-based hidden Markov model, Meta-MEME requires that various parameters be set. By default, Meta-MEME employs reasonable values for these parameters. However, when submitting a job to the server, you may choose to override the default settings. The following list explains each parameter and gives its default value.

Model building

• Model topology
  By default, Meta-MEME builds models that have a linear topology, in which the motifs are arranged like beads on a string. If, however, you believe that the family you are interested in contains repeated or shuffled elements, you may wish to build a model in which every motif is connected to every other motif. Note that completely connected models cannot be used to create multiple alignments.
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• Motifs
  By default, Meta-MEME includes in the hidden Markov model all the motifs that appear in more than half of the sequences in the training set. You may choose instead to include more or fewer of the given motifs.
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• Spacer models
  Meta-MEME models the non-motif, spacer regions of the given family using HMM states with self-loops on them. Because a single such state yields an exponential distribution of spacer lengths, Meta-MEME can use several such states in succession to give a more bell-shaped distribution of spacer lengths. Note that these multi-state spacer models are only useful in conjunction with total probability scoring.

Homology detection

• Scoring
  By default, when Meta-MEME uses a model to search a sequence database for homologs, the sequences are scored using the Viterbi algorithm. This algorithm computes the most likely path through the model, given the sequence. Alternatively, you can ask Meta-MEME to compute the total probability of the sequence with respect to all paths through the model.
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• Score threshold
  Meta-MEME reports homology log-odds scores in bits. Typically, Meta-MEME only reports scores for sequences that score above zero. You can set the score reporting threshold to some other value. Note that, regardless of the threshold you select, the Meta-MEME server will report at least 10 scores and at most 1000 scores.
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• Minimum number of sequences
  This parameter determines the minimum number of homology scores reported by Meta-MEME. The default value is 10.
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• Maximum number of sequences
  This parameter determines the maximum number of homology scores reported by Meta-MEME. The default value is 100.

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Please send comments and questions to Charles E. Grant at @METAMEME_CONTACT@.