diversity

diversity uses a Bayesian approach to detect multiple modes of protein-DNA binding from high throughput ChIP data. It is available both as a web based application and as a downloadable software.


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Input:
Input can be in FASTA or BED format. Sample input can be downloaded and run on diversity web server.

In case of a FASTA file,

Sample FASTA input
Sample BED input

Output:
Output is saved in OUTPUT directory after the run is complete. The documentation provides details about the files which are produced in the output directory.

Please refer to the info.txt for detailed results.

Sample Output for FASTA input
Sample Output for BED input

Select the format of the input file. It can be in bed or fasta format.
Can be fasta or bed depending on what format is chosen. This is the only compulsory input for running diversity. (fasta sample) (bed sample)
Minimum number of modes. Default value: 3
Maximum number of modes. Default value: 10
Starting width of the motifs. Default value: 12
Minimum motif width. Default value: 6
Mask repeats in sequences. By default it masks.
Include reverse strand while training. By default it includes.
Enter your name.
Enter your email address.
Zero or one occurrence of motif per sequence.
0 means all sequences must have a motif, 1 means all sequences may not have a motif. Any value between 0 and 1 implies probability of a sequence not having a motif. Default value: 0
Click 'Yes' to save likelihood plots of every model learned. Default: likelihood plots are not saved
Number of models to be learned while training. Only the best model is considered. Default value: 5
Reset all fields in the form
Submit for execution
Upon submission of the form, a link would be provided. This link displays the status of execution. The status can be QUEUED, RUNNING or COMPLETE. When complete, the results can be downloaded. The results would be saved for 48 hours after execution is over.


The example fasta and bed files can be downloaded and used as input.
In case the input file is in BED format, and the genome is hg19, then the web server takes longer time to create the OUTPUT.