TranScout: prediction of gene expression regulatory proteins from their sequences.

Abstract

The advent of genomics yields thousands of reading frames in search of function. Identification of conserved functional motifs in protein sequences can be helpful for function prediction. A database and a classification of reported DNA-binding protein motifs has been designed. A program ('TranScout') has been developed for the detection and evaluation of conserved motifs in prokaryotic and eukaryotic sequences of proteins with a gene regulatory function. The efficiency of the program is shown in a benchmark against a database obtained from SWISS-PROT without the protein sequences used to train the program. All motifs were detected with a mean average sensitivity of 0.98 and a mean average specificity of 0.92. The program is freely available for use on the internet at http://luz.uab.es/transcout/. The user can find additional information at this site.