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Cis-analysis - Teaching Server
Exercise
Description
Output legends
Article abstracts
Upload promoter file, containing multible promoters in FASTA format
pattern length
6
7
8
Method:
Saco patterns
Gibbs Sampler
Saco patterns - Parameters
MODE:
If left unchecked Kolmogorov-Smirnoff statistics is performed on the input sequences only.
If checked: hypergeometric statistics is perform on the imput set (positive) compared to all
Arabidopsis
promoters (26828 promoters).
The cutoff for Saco_patterns (Only one cutoff is used)
0.3
0.0
0.25
0.32
0.35
0.4
0.5
Kolmogorov-Smirnoff cutoff (0.3-0.6 is a reasonable range)
2
0.0
0.5
1
3
5
Hypergeometric statistics (a cutoff of 2 means significant at a 99% confidence level).
Gibbs Sampler - Parameters
Number of runs:
5
10
25
50
Number of iterations pr. run:
100
250
500
1000
Number of pseudo counts
1
2
5
10
GETTING HELP
Server problems:
This file was last modified Monday 2nd 2008f June 2008 13:09:56 GMT
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