The Gibbs Motif Sampler for DNA

The Gibbs Motif Sampler (for DNA)

Due to current server restrictions, total number of sequences is restricted to 1000. The maximum length of an individual sequence is limited to 10000.

Please enter the requested information. Items marked with an * are required. Your results will be mailed to you.

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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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Please enter the data sequence: (FASTA format) * >hspX complement(2278496..2278930) Rv2032 2279127..2280122 5UTR genome coordinates=2278931-2279126 length=196 ttgatgcctcctaatcgatggaaacggatgcctttgatccgaccagcccatcgtggccag ggctagggacagaagtccccgaagcgcgggccatttgtccgcgcccgtcggtgatccact tggggaccattgaccctgttgtctgccaaccgccgttcagaaagatcggggtgatatcga acagcggaggttgatc >Rv3130c complement(3494972..3496363) Rv3131 3496548..3497546 5UTR genome coordinates=3496364-3496547 length=184 ggtcagcgccttccccggtgatccggattatctgcaaccgtcagtaccactctccgctgc gaggagccgttgaggcagggccaaaggtcctccgctggcgagccttcgtgctctgccacc gcggctgtcgacgcgcgatccttaatagatgaccgcagccgttgatgggaaaggcccggc agcc >Rv2005c complement(2250994..2251881) otsB 2252000..2255983 5UTR genome coordinates=2251882-2251999 length=118 ctcattctcccttcgcctcgagcaacgctatgaaccgggacagtcaccggtcatgaggct ttagtccccaatcggacggccaaccgaccatgattggattcgacgcccgaatccaagc >Rv2623 2949591..2950484 Rv2622 2948634..2949455 5UTR genome coordinates=2949456-2949590 length=135 tccattgaggacctaagcccgttgggctagtgacaaacgcctcctgagcaaaaccctcct cccccgttaccgtcgtgcggtagggacaagccacatcggccgagcgggcgatcagccaac gacaggaggaccgcg >narK2 complement(1964181..1965368) Rv1738 1965655..1965939 5UTR genome coordinates=1965369-1965654 length=286 cgacacgatccggggtctcggactccggcgaactccgcgccccgcccggacagccatgcg ctaaccctggcttcgatggcgccggctcagttagggccggaagtccccaatgtggcagac ctttcgcccctggcggacgaatgaccccagtggccgggacttcaggccctatcggagggc tccggcgcggtggtcggatttgtctgtggaggttacaccccaatcgcaaggatgcattat gaccagcgagctgagcctggtcgccactggaaaggggagcaacatc >Rv1733c complement(1959853..1960485) Rv1734c complement(1960772..1961014) 5UTR genome coordinates=1960486-1960771 length=286 cgctgtgaattgctcgtggctcctagggtcgttcggccttggggctggggacgtcggtca cgaatggctgggcgccgtgcatatcgggtgaaccgggcgtcgaacaagcgaagttttatt gtcggataagggactttcgccccttcccgcctgctgtgtttggtggcagtattggtgata ccggggaaacccggtgatctgcccgaagtgctgggcgattgagcgggtatgtacacccgg tttgacctaccgtcccaagacggggctaccgccttcgggcagatcc >Rv3127 3492144..3493178 Rv3125c complement(3490473..3491648) 5UTR genome coordinates=3491649-3492143 length=495 cgcaaccccagcccaatcagccgcccagaagggtctcgtacaagggttaactaaacaatc gttaccgaatgaatcgacacatcgtgacgcaccgatggctcagcacgccggacttctaga acaacgagcacaacggatatgatgcggcaggcatcttcatggattgtcaatgacagccca aaccgccttcggccactggcattggtgcactgcaccgtgcgccattcgtggcgacaactg cgagcgggagcgggaccaaggatgatggtcccggtcgcgacgggcgcgatcccgctccgg agtggtcaacgcatcaaacgacaaagcgctcagctcatcgaccgcagcatcgagccggtc cagcgccgcgaccaaactagaattctcgcgcagacaccgctgaaacgacagtgacgcaag ggatttcattgagaggaccaatgaccctatttgatcaaaccggatgaccataccgtcaac gttgtggacatacag

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: (motif,start,end... ex: 1,1,8)		Reduced Alphabet: (motif,start,end... ex: 1,1,8)
Local composition: (motif,start,end,pal... ex: 1,1,8,1)		Direct repeat pos: (motif,start,end... 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) >BLOCKS 0.05 0.30 0.30 0.30 0.05 >
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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