PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region

Abstract

Bacterial small-RNA (sRNA) sequences are functional RNAs, which play an important role in regulating the expression of a diverse class of genes. It is thus critical to identify such sRNA sequences and their probable mRNA targets. Here, we discuss new procedures to identify and characterize sRNA and their targets via the introduction of an integrated online platform named PresRAT (Prediction of sRNA and their Targets). PresRAT uses the primary and secondary structural attributes of sRNA sequences to predict sRNA from a given sequence or bacterial genome. PresRAT also finds probable target mRNAs of sRNA sequences from a given bacterial chromosome and further concentrates on identification of the probable sRNA-mRNA binding regions.Using PresRAT we have identified a total of 60,518 potential sRNA sequences from 54 bacterial genomes and 2447 potential targets from 13 bacterial genomes. We have also implemented a protocol to build and refine 3D models of sRNA and sRNA-mRNA duplex regions and generated 3D models of 50 known sRNAs and 81 sRNA-mRNA duplexes using this platform. Along with the server part, PresRAT also contains a database section, which enlists the predicted sRNA sequences, sRNA targets and their corresponding 3D models with structural dynamics information..

Investigating the impact of insertion sequences and transposons in the genomes of the most significant phytopathogenic bacteria

“…Therefore, for those elements that were altered in expression in the previous analysis, we decided to investigate the possibility of these transposable elements encoding small regulatory RNAs. All Tns sequences and IS sequences under positive selection pressure were evaluated for sRNAs prediction using four distinct methods: INFERNAL [ 31 ], RNAz [ 32 ], PresRAT [ 33 ] and Oasis 2 [ 34 ]. Only sRNAs that had the same target in the different algorithms and had sampled probability values equal to zero (CopraRNA P -value=0) were considered true.…”

Regulation of biofilm formation by non-coding RNA in prokaryotes

“…Other ncRNA prediction tools such as sRNAPredict2 evaluates the information based on RHO-independent terminators. Another online platform, PresRAT uses attributes of sRNA sequence to identify sRNA ( Kumar et al., 2021 ). The RNA-seq (RNA sequencing) method, which employs cDNA sequencing has been extensively used to identify non-coding RNA in bacteria.…”

Microbial Small RNAs – The Missing Link in the Nitrogen Cycle?

“…Existing tools predict sRNA targets based on sequence, thermodynamic scoring of mRNA-sRNA mixed duplexes and RNA secondary structure. However, the accuracy of these tools is highly variable, and their use is complex (Kumar et al, 2020). Therefore, we can assume that many sRNAs remain undiscovered, especially in organisms that are less studied.…”