Abstract
Occurring at cytosine (C) of RNA, 5-methylcytosine (m5C) is an important post-transcriptional modification (PTCM). The modification plays significant roles in biological processes by regulating RNA metabolism in both eukaryotes and prokaryotes. It may also, however, cause cancers and other major diseases. Given an uncharacterized RNA sequence that contains many C residues, can we identify which one of them can be of m5C modification, and which one cannot? It is no doubt a crucial problem, particularly with the explosive growth of RNA sequences in the postgenomic age. Unfortunately, so far no user-friendly web-server whatsoever has been developed to address such a problem. To meet the increasingly high demand from most experimental scientists working in the area of drug development, we have developed a new predictor called iRNAm5C-PseDNC by incorporating ten types of physical-chemical properties into pseudo dinucleotide composition via the auto/cross-covariance approach. Rigorous jackknife tests show that its anticipated accuracy is quite high. For most experimental scientists’ convenience, a user-friendly web-server for the predictor has been provided at http://www.jci-bioinfo.cn/iRNAm5C-PseDNC along with a step-by-step user guide, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the approach presented here can also be used to deal with many other problems in genome analysis.
Highlights
Post-transcriptional modifications (PTCM) of RNA plays a paramount role for the metabolism processes of RNAs, such as for their splicing export, immune tolerance, and transcription [1,2,3]
More than 100 distinct PTCMs have been identified in tRNAs, rRNAs, Mt-tRNAs, miRNAs, lincRNAs, miscRNAs, protein-coding genes, pseudogenes, etc
The m5C modification is well investigated in DNA, but the corresponding studies in cellular RNA were mainly confined to tRNA and rRNA [6]
Summary
Post-transcriptional modifications (PTCM) of RNA plays a paramount role for the metabolism processes of RNAs, such as for their splicing export, immune tolerance, and transcription [1,2,3]. In a pioneering study, Feng et al [8] proposed an interesting method to identify RNA m5C sites via the powerful PseKNC approach [9,10,11].
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