EcoGram: Syntactic Recognition of Regulatory Regions in E.coli


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Here we offer EcoGram, a grammar-based computational method to find putative binding sites in DNA regulatory regions for a given set of regulatory proteins.

In its current form the user is required to know the precise location of the inititation of transcription (+1). Alternatively, the user might rely on a predicted promoter.

When reporting results with this method please refer to:

Thieffry, D., Rosenblueth, D. A., Huerta, A. M., Salgado, H. and Collado-Vides, J. (1996). "Definite-Clause Grammars for the analysis of cis-regulatory regions in E. coli." In: Altman, R., Dunker, K., Hunter, L. and Klein, T. (eds.). Proceedings of the Pacific Symposium on Biocomputing'97. World Scientific, Singapor, pp. 441-452.

Or refer to:

Rosenblueth D.A., Thieffry D., Huerta A.M., Salgado H. y Collado-Vides J. (1996) "Syntactic recognition of regulatory regions in Escherichia coli" CABIOS 12: 415-422.

Results are treated confidentially. In the future we will be sending the results by e-mail.


Please indicate:


Your name:
email address:


Select one or several proteins in the following list:


AraC

ArgR

CRP

FNR

GlpR

LexA

MalT

MetJ

PhoB

PurR

PutA

TyrR

Paste here your sequence in uppercase and the beginning of transcription in lowercase: sequence.name \SEQUENCE [a,t,c,g] SEQUENCE\

Note: Include one line per sequence without break-lines.

Example :

FOO_SEQ \ GTATATACACTGATCACAGCaTAACTGTATATACTCATACGTCCGTGAT \

         

Warning ! EcoGram is time-consuming, especially if you have pasted many and/or long sequences. We will be offering the service of email-output soon.


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for web questions victor@ccg.unam.mx & amhuerta@ccg.unam.mx , last modification: Oct-16-2006.