IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico.

ABSTRACT:

Background

Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal with IRES elements.

Results

We designed an IRES search system, named IRSS, to obtain better results for IRES prediction. RNA secondary structure prediction and comparison software programs were implemented to construct our two-stage strategy for the IRSS. Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted stru

SUBMITTER: Wu TY 

PROVIDER: S-EPMC2698906 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature