IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES)

Abstract

Cellular mRNAs are predominantly translated in a cap-dependent manner. However, some viral and a subset of cellular mRNAs initiate their translation in a cap-independent manner. This requires presence of a structured RNA element, known as, Internal Ribosome Entry Site (IRES) in their 5′ untranslated regions (UTRs). Experimental demonstration of IRES in UTR remains a challenging task. Computational prediction of IRES merely based on sequence and structure conservation is also difficult, particularly for cellular IRES. A web server, IRESPred is developed for prediction of both viral and cellular IRES using Support Vector Machine (SVM). The predictive model was built using 35 features that are based on sequence and structural properties of UTRs and the probabilities of interactions between UTR and small subunit ribosomal proteins (SSRPs). The model was found to have 75.51% accuracy, 75.75% sensitivity, 75.25% specificity, 75.75% precision and Matthews Correlation Coefficient (MCC) of 0.51 in blind testing. IRESPred was found to perform better than the only available viral IRES prediction server, VIPS. The IRESPred server is freely available at http://bioinfo.net.in/IRESPred/.

Continued circulation, recombination and evolution of the ancient subcontinent lineage despite predominance of the recent arctic-like lineage rabies viruses (RABV) in India

“…The RTD-based alignment-free method is based on frequency of k-mers and the relative order in which the k-mers occur in the sequences. The method is proved to be accurate and computationally efficient for analysis of gene and/or genome data as validated using a variety of human viruses causing NTDs such as Mumps, Rhino, Dengue and West Nile viruses [33, 34]. Regardless of the method used, the phylogenetic trees constructed using both N and G genes showed RABV isolates from this study belonged to two distinct linages namely Arctic lineage and Indian subcontinent lineage.…”

The Evolution of Line-1 in Vertebrates

“…The IRESPred webserver, which detects IRES in a sequence of interest by searching for sequence and structural features found in known nuclear and viral IRES sequence (Kolekar et al 2016), predicts the presence of IRES in 32 out of 36 long IGR sequences. The program failed to predict the presence of IRES in only two frog and two fish elements.…”

“…Putative Internal Ribosome Entry Sites (IRES) were identified using the IRESPred tool, which uses 35 features based on sequence and structural properties to predict the presence of cellular or viral IRES (Kolekar et al 2016). We also used the Viral IRES Prediction System (VIPS), which uses the secondary structure of four groups of known viral IRES to predict putative viral IRES (Hong et al 2013).…”

Translational Control Mechanisms in Persistent Pain

“…Finally, internal ribosome entry sites (IRESs) mediate cap-independent translation initiation [32]. IRESs are present in many mammalian mRNAs [32–34], but their functional role remains elusive.…”