The Gibbs Motif Sampler (for DNA)

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If you plan on running large jobs or many multiple runs, we encourage you to obtain the stand-alone version of Gibbs. Gibbs source code and binaries for Linux, MS Windows (using Cygwin), Solaris, Solaris.x86 and MAC OS-X are available: here.

  • Annotated Examples

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    How to enter data?
    Email Address:
    Please enter the data sequence: (FASTA format) *
    Prokaryotic Defaults Eukaryotic Defaults
    Sampler Mode: Site Sampler Motif Sampler
    Recursive Sampler Centroid Sampler
    No. of different motifs (patterns): Max sites per seq: (recursive sampler)
    Motif Width(s):* Est. total sites for each motif type:
    Burn-in period: Samples:
    Align Centroid Model: Number of seeds:
    Palindromic pos:
    ex: 1,1,8)
    Reduced Alphabet:
    ex: 1,1,8)
    Local composition:
    ex: 1,1,8,1)
    Direct repeat pos:
    ex: 1,1,8)
    Reverse complement: Background Model:
    Fragmentation: Max Frag. Width:
    Frag. from center: Wilcoxon signed-rank test:
    Sample Motif Width(s): Near Opt. Soln.:
    Output for dscan: Frequency Soln.:
    Aligned Seqs: MAP maximization:

    Please enter Prior information: (optional, leave blank for uninformed priors)

    Please enter the Spacing Model: (optional, leave blank for a uniform spacing model)
    Pseudosite wt.(%): Pseudocount wt.(%):
    Plateau period: Adjustment period:
    Max iterations: Near opt. cutoff(%):
    Random number seed: Calc. default pseudocounts:

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