CONSENSUS	MEME	GIBBS sampler	CORESEARCH
option setting	option setting	option setting	option setting

return to the top page

Consensus Option Setting

Lenght of search motif
Number of matrices to save
Number of cycles if 0 or more motifs per sequence are required
Number of cycles if 1 or more motifs per sequence are required
Minimum distance between words
Terminate indicated number of cycles after most significant alignment
Use designated prior frequencies
Seed with first sequence and proceed linearly through list
1:Ignore the complementary strand 2:Include both strands as separate sequences 3:Include both strands as a single sequence(i.e., orientation unknown) 4:Assume that the pattern is symmetrical	1 2 3 4
1:Save the top progeny for each parental matrix 2:Save top progeny matrices regardless of parentage(the default)	1 2
Number of top matrices to print
Number of final matrices to print

Back

---

MEME Option Setting

MAXimum length of search motif (<= 300)
MINimum length of search motif (>=2)
MAXimum number of sites for each motif(<=300)
MINimum number of sites for each motif(>=2)
MAXimum number of motifs to find
Motif distribution menu 1: One occurence per sequence 2: Zero or one occurence per sequence 3: Any number of repetitions per sequence	1 2 3
Stop if E-motif value is greater than
Maximum EM iterations to run
Do not adjust motif length using multiple alignment
Gap opening cost for multiple alignments
Gap extention cost for multiple alignments
Do not count end gaps in multiple alignments
Use complementary strand
Force palindromes
Output results in text format

Back

---

Gibbs Option Setting

Length of search motif
Expected number of elements for each type
Near optimal cutoff (%)
Number of cycles between shifts (sites sampler)
Maximum number of iterations for each seed
Maximum number of sampling runs
Give seed for random number generator
Pseudo count weights
Pseudo site weights (sites sampler)
DO NOT use fragmentation (i.e., column sampler)
Use element order in probabilities (sites sampler)
Randomly shuffle input sequences
DON'T remove protein low complexity regions
Output wilcoxon rank test information (motif sampler)

Back

---

Coresearch Option Setting

1. Length of serach motif
2. Conservation of the sequences in which a motif must occurs (%)
3. Number of highly conserved positions and allowed distances permitted in a motif
4. Conservation of sequences in which motifs with highly conserved positions must occur
5. Maximum number of motif sets for optimal calculation method
6. Minimum motif set conservation to select a motif
7. Maximum number of best motif sets to select for each motif
8. Length of region left of tuple for region alignment
9. Length of region right of tuple for region alignment
10. Maxmum number of position sets per set for optimum calculations
11. Minimum region conservation for a position set
12. Minimum similarity of motif with consensus motif to be included in a consensus
13. Minimum similarity of motif with consensus core string to be included in a list of possible cores
14. Gap penalty
15. Gap length factor
16. Distance score for A/G and C/T matches
17. Distance score for A/T matches
18. Distance score between gap and nucleotide
19. Sequence weight factor
20. Number of shuffles

Back

---