RiCES: Rice Cis-Element Search Tool

	RiCES: Rice Cis-Element Searcher Rel. 07n19

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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.

RiCES has been updated on 19, Nov. 2007. The major improvements are:

The system has been named. RiCES is derived from "RIce Cis-Element Search".
RiCES now accepts multipe gene ID systems popular in research of Oryza, including TIGR locus ID, TIGR TU ID, IRGSP locus ID, IRGSP locus ID and GenBank accession number. Any IDs will be automatically and internally translated into TIGR TU ID. As RiCES is design to perform analysis based on TIGR ID, IDs without corresponding TIGR TU ID will be ignored (See document for detail).

The new paper describing RiCES has been published. [PubMed]

        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.

View Result of Former Analyses

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.

Required Items

General Setting

Do combined motif analysis		Yes No
Source of preliminary cis-element candidate list		MEME is temporary unavailable due to system updating. Sorry for inconvenience. MEME Built-in list User-defined motif list (see below)
Reference Sequence Data	Region	Use bps of	upstream region
		Use bps of	downstream region
		Use whole of	coding region
	Gene	Adjust Reference Size to Target TU list
Association Rule Output Threshold (Minimum)			Confidence: Lift:

User's Gene(TU) List

Input IDs of transcription units to be examined
[See Example]

Optional Items

Options for MEME

Following options are ignored unless "use MEME" option is selected in general setting.

Use recommended parameters for MEME (see below)
Use following parameters for MEME
- 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)

Extra options

Motif list

Keep this column empty if you just want to find novel cis-element candidates from TU with list.
If you like to evaluate extraordinal cis-element candidate, input their sequences here. In this case, you must select "User-defined motif list" in general setting.

Remarks

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

mod=zoops
minw=6
maxw=8
nmotifs=100

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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RiCES: Rice Cis-Element Searcher