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RiCES: Rice Cis-Element Searcher

Rel. 09317
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RiCES Official Site (IRRI)
RiCES Mirror Site (NIAS)
GCP IRRI Portal
Rice Gene ID Converter

RiCES is a cis-element searching tool optimized for rice (Oryza sativa) genome.

It takes as input a list of identifiers of transcription unit IDs of Oryza sativa, defined in Pseudomolecule corresponding to KOME full length cDNA clones, and returns a list of cis-element sites that appear to be shared across the listed gene loci. The motif searching program, MEME, is applied in the front step of the analysis.

This tool was developed by Dr. Koji Doi, National Institute of Agrobiological Sciences (NIAS), with funding from the Generation Challenge Programme.

View Result of Former Analyses

Input Analysis ID here:

New Analysis

To perform analysis, please input TU IDs in the box appearing in the form below. The tool will search corresponding cis-element candidates, and shows them as a html page or a xml page. Further information can be found in the document.

User's
Gene (TU)
List
Input IDs of transcription units to be examined
[See Example]

Reference
Sequence
Data

 Region Use    bps of upstream region
downstream region
Use whole of coding region
Gene Please select prepared list, or 'user specified list' to specify your own reference list.
In case of 'user specified list', put gene IDs of your list into the box below.
User's reference TUs

Adjust Reference Size to Target TU list

Preliminary Candidate Source


Complementary sequences are also focused 		Built-in list (default)
MEME
 Use recommended parameters (see below)
  • Minimum motif length[bp] (6, 7 or 8: default 6)
  • Maximum motif length[bp] (6, 7 or 8: default 8)
  • MEME search algorithm (default zoops)anr zoops
  • MEME extra parameters (Ex. nmotifs=50)
Use customized parameters→
User-
defined
motif
list
  • If you like to evaluate extraordinal cis-element candidate, input their sequences here.

Association Rule Output Threshold (Minimum)

 Confidence: Lift:

Extra options

Remarks
'Recommended' parameters are as follows. The definition is base on the policy of developers of this tool.

DO IT NOW

CLICK APPLY BUTTON to start analysis.

Reference

        Doi K, Hosaka A, Nagata T, Satoh K, Suzuki K, Mauleon R, Mendoza MJ, Bruskiewich R, Kikuchi S, 2008. 
        "Development of a novel data mining tool to find cis-elements in rice gene promoter regions." 
        BMC Plant Biology 8:20. [PubMed]
        

        Timothy L. Bailey and Charles Elkan, 1994. "Fitting a mixture model by
        expectation maximization to discover motifs in biopolymers",
        Proceedings of the Second International Conference on Intelligent
        Systems for Molecular Biology, (28-36), AAAI Press

Disclaimer

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