UlTRaSCAN-An algorithm for prediction of pattern(s) in untranslated regions of eukaryotic mRNAs

Abstract

Many <i style="">cis</i> acting elements have been identified in the 3' and 5' untranslated regions (UTRs) of eukaryotic mRNAs. These <i style="">cis</i> acting elements are found to play vital roles in pre-mRNA processing, nucleo-cytoplasmic transport of processed mRNAs, determining the efficiency of translation of mRNAs and their stability and degradation in the cytoplasm. UTRScan utility has been used to identify these patterns in mRNAs. However, the UTRScan is not very sensitive and also not highly specific. It often generates many false positives as it scans the whole mRNA including the coding sequence. The authors have developed a new algorithm and an Internet based web application tool, named UlTRaSCAN, which overcomes these limitations and proved to be highly specific and sensitive in detecting patterns in UTRs. The new algorithm identifies these <i style="">cis</i> acting elements only in the 3' and 5' UTRs of eukaryotic mRNA/DNA sequences. The sensitivity is more than doubled and the specificity is increased, close to 100%. The UlTRaSCAN also minimized the false positives to almost 0% and the false negatives to large extent.<b style=""> </b>