Assesses 13C chemical shifts (CS) assignment of RNA. 13Check_RNA is able to adjust 13C CS systematic errors in 13Cexp data based on a method proposed by Aeschbacher. This software corrects errors that interfere with establishing a reliable relationship between experimental data with macromolecular structure.
Identifies genetic variants targeting m6A modification sites. m6ASNP is a web server that annotates variants by m6A function. The software was designed for predicting if methylation status of an m6A site is altered by variants around the site. It can serve as a supplemental method to run in parallel with other annotating tools to comprehensively predict the function of the variants, for both synonymous and non-synonymous, in the high-throughput sequencing studies of diseases.
Identifies read alignments, single nucleotide polymorphisms (SNPs), hyper-editing patterns, and expression levels. RepProfile is based on the expectation maximization (EM) algorithm. It alternates between averaging over hidden variables and estimating the hyper-editing, SNPs and expression. The tool considers one repeat family at a time. It permits to discover RNA duplexes with hundreds of edited positions, where other methods find few or no sites.
Allows users to predict chemically modified nucleosides in tRNA sequences. tRNAmodpred can provide valuable initial predictions that could be a starting point for experimental analyses. Its predictions are based on detection of homology to known RNA modification enzymes. The quality of these predictions depends on the data about modified tRNA sequences and RNA modification enzymes. The method of this tool is also applicable to other conserved RNA molecules (such as rRNA).
Allows users to predict and classify UMs from tRNA sequences or whole genome of any organism. tRNAmod contains two different prediction options available in tRNAmod: (1) Sequence-level prediction and (2) Genome wide prediction. For the the sequence-level prediction, it requires tRNA sequences, and for the Genome-wide prediction, it requires whole genome sequence.
Identifies RNA modifications in Homo sapiens transcriptome. iRNA-PseColl is a web server which allows to identify N1-methyladenosine (m1A), N6-methyladenosine(m6A) and 5-methylcytosine modifications (m5C). The software was developed by incorporating collective effects of nucleotides into pseudo K-tuple nucleotide composition (PseKNC). The jack-knife test was used to examine the quality of the method.
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