model (70). We performed a search for regulatory sites and splicing signals using the TRANSFAC database (http://www.biobaseinternational.com/pages/index.php? id=transfacdatabases). Rodent and primate 5′-UTRs were computationally folded by program Afold (71) to predict potential IRES stable structures. The predicted minimum free secondary structure energy was calculated using our implementation of the dynamic programming algorithm described by Zuker (72), which employs nearest neighbor parameters for the evaluation of free energy.
