REMmatch program: finding potential hormone responsive elements

Nikolai Aksenov1, Alex Lyakhovich2
1nikolay.aksenov@plantphys.umu.se, Umea University; 2alexlyak@umich.edu, University of Michigan

REMmatch program ( http://www.math.wisc.edu/~karp/REMmatch.exe) is aimed to make a quick preliminary screening of any sequence database for searching potential hormone responsive elements (HRE). To test this program we have analized a number of promoter regions for a group of growth factors and made a screan for responsive elements to steroid hormones and hormone-like chemicals. Our experiments show that more than 70% of predicted sequences are indeed related to hormone responsive elements. We compared our data with those obtaned from other known programs including TESS (Transcription Element Search Software, http://www.cbil.upenn.edu/tess/) and Match (Matrix Search, http://compel.bionet.nsc.ru/cgi-bin/MoMatch/momatch.pl). TESS findings resulted in 65% similar to REMmatch findings. Better prediction was made when screaning 5 flancked regions (80%). Using REMmatch we were able to find more unknown HREs than using TESS or Match software. These predicted HREs were further confirmed to be responsive elements for several hormones. We are now in a process of embedding a database for hormone responsive elements to our program which will be freely available at http://www.math.wisc.edu/~karp/datasearch.