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Matrix associated regions - Need a prediction program (Apr/03/2009 )

I'm looking for a computation tool that can be used to predict Matrix
associated regions (MARS or S/MARS). So basically I want to paste a sequence and
have a software program analyze the sequence and list any possible attachment sites.
Alll the online sites I have examined are dead links.
Any suggestions?


You can look up this paper: A comparative study of S/MAR prediction tools. BMC Bioinformatics. 2007 Mar 2; Evans K, Ott S, Hansen A, Koentges G, Wernisch L. Basically, the conclusion is that none of the methods worked well. You can still try the SMARTest by Genomatix. It has a 7-day free trial period. My experience is that the SMARTest will only detect regions that are extremely A/T rich (>65%).


Thanks for the info Rockfan!