Key result
The IRSS tool demonstrated a low error rate and up to 72.3% sensitivity in predicting IRES elements using appropriate parameters.
IRSS is a novel web-based bioinformatics tool that combines minimum free energy and RNA alignment modeling to predict viral IRES secondary structures with up to 72.3% sensitivity.
May support IRES research tools; leaves open clinical adoption without prospective validation.
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 structures. After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters. CONCLUSION: IRSS is freely available at this website http://140.135.61.9/ires/. In addition, all source codes, precompiled binaries, examples and documentations are downloadable for local execution. This new search approach for IRES elements will provide a useful research tool on IRES related studies.
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Wu et al. (2009) studied Viral genomes (IRES prediction). IRSS (IRES search system) was evaluated on Sensitivity of IRES prediction. The IRSS tool demonstrated a low error rate and up to 72.3% sensitivity in predicting IRES elements using appropriate parameters.
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