Central mode tests regions centered on the sequence for enrichment. This is useful for ChIP-seq data as you expect your ChIPed TFBS to appear in areas of maximum tag density. If you prepare sequences centered on these positions of maximum confidence then CentriMo can help confirm that your expected motif does correspond to the ChIPed TF.

Local mode tests all possible regions for enrichment. The downside is this mode must do many more tests than central mode which makes it slower and also less sensitive in the central regions due to the larger multiple test correction.

The binomial test compares the number of sequences that had their best matches in the region to the expected number of sequences under the assumption that matches would be randomly distributed.

Adding a second comparative dataset allows use of the Fisher exact test (FET) to sort the regions found by the binomial test. The FET compares the number of sequences that have their best matches in the region to the number found in the comparative set.

Select a file of FASTA formatted DNA sequences or paste in actual FASTA formatted DNA sequences to search for enriched regions.

See the sample sequences to get an idea of input that works well for CentriMo.

Select a file of FASTA formatted DNA sequences or paste in actual FASTA formatted DNA sequences to compare to the other sequence set.

See the sample sequences to get an idea of input that works well for CentriMo.

CentriMo can use databases installed on the server or search a user uploaded database in MEME DNA motif format by selecting the "Upload Your Own Database" option. For more information browse the supported databases.

An uploaded database is a normal MEME DNA motif file with lots of motifs. The uploaded database must be smaller than 5MB.

The email is used to notify you of your results.

The job description will be included in the notification email you receive and in the CentriMo output.

By default CentriMo will determine the background Markov model from the provided sequences. Alternately a file containing a background model may be input here.

The downloadable version of the MEME Suite contains a script named "fasta-get-markov" that you can use to create background model files in the correct format from FASTA sequence files.

Choose between single and double strand scanning. The flip RC position option causes any matches on the reverse strand to have their position mirrored around the center of the sequence. This option was enabled by default in the original released version of CentriMo.

Specify a minimum score for a match to be considered. If a sequence does not have any matches which meet this minimum score for a given motif, then that sequence will not be considered for that motif.

If the "optimize score" option is selected then all distinct scores for matches that did better than the minimum score will be tested as alternative minimum score thresholds. Enabling this option will slow down the program and increase the multiple testing correction.

This option limits the maximum region size that CentriMo will test. This option is useful if you have sequences longer than the normal 500bp and can help cut-down the multiple testing correction. When this option is not supplied CentriMo will test region sizes up to one less than the maximum number of places that a given motif can align to the sequence.

This is the E-value threshold for reporting enriched regions for motifs. If multiple enriched regions overlap then the region with the best p-value and smallest size will be output.

This option enables you to store the sequence identifies which have their best match in the best region for each motif. This option can potentially make the CentriMo output file size much larger.