PLANTCIS

PLANTCIS is a web tool for finding cis-regulatory elements (CREs) in plant gene promoters. PLANTCIS uses the PLACE database (Higo et al., 1999) and novel described CIS elements (Phase II). The software performs statistical analysis to validate if a given CRE has a non-randomic pattern in the promoter region of a given gene. CREs that are statistically significant in the promoter(s) of a gene or group of genes with a specific query, i.e.,  response to iron excess, drought, cold, salinity or flooding are indicative of association of the CRE with the studied function and can be further investigated in validation studies.

Click here to acess PlantCis:

http://177.11.48.143/~microsat/cis_input2.html

http://microsatellite.org/cis_input.html

Click here to acess SSRLocator:

http://177.11.48.143/~microsat/ssr.php

http://microsatellite.org/ssr.php

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SSRLocator

A computing tool with an interface for Windowsusers was developed, called SSR Locator. The application integrates the following functions:
- (i) detection and characterization of SSRs and minisatellite motifs between 1 and 10 base pairs; - (ii) primer design for each locus found;
- (iii) simulation of PCR (polymerase chain reaction), amplifying fragments with different primer pairs from a given set of fasta files;
- (iv) global alignment between amplicons generated by the same primer pair;
- (v) estimation of global alignment scores and identities between amplicons, generating information on primer specificity and redundancy.
                    

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