MODOMICS

[…] DIP (), as well as new databases such as miRCarta (). The new MSDD () links miRNA SNPs to diseases while EVLncRNAs () and MNDR () also major on disease links for non-coding RNAs. The well-established MODOMICS database of RNA modifications () is the subject of an update paper which, among other developments, reports on the availability of liquid chromatography/mass spectrometry data for modified nu […]

[…] s by taking into account the 40 modifications identified in BCG tRNA (; ), predicted modifications by tRNAmod (http://crdd.osdd.net/raghava/trnamod/) and comparisons with tRNA sequences catalogued in Modomics (http://modomics.genesilico.pl/). The exact masses of these potential modified oligomers and their c1 and y1 ion fragments were calculated. Selected reaction monitoring (SRM) worklists were c […]

[…] ated signatures in thus prepared RNA-seq libraries, the reads were mapped onto a minimal target genome consisting only of rRNA and tRNA sequences. The respective sequences have been obtained from the Modomics database () and do thus not contain any unspliced or unprocessed sequences, but, importantly, sequences of known modifications status. This is in some contrast to the previously published HAM […]

[…] owed evidence for demethylation of both an expected m3C32 modification, and an unexpected m1A58.ARM-Seq also predicted m1A58 modifications for five yeast tRNAs in isodecoder groups not represented in Modomics and unmodified A58 for three others, with primer extensions confirming m1A58 for Leu-GAG and unmodified A58 for Arg-CCG and Gly-CCC (, ). The final tRNA not represented in Modomics, Pro-AGG, […]

[…] Xcaliber software. The tRNA genomic sequences were obtained from the Genomic tRNA Database (http://gtrnadb.ucsc.edu/).E. coli tRNA sequences with post-transcriptional modifications were obtained from Modomics (http://modomics.genesilico.pl/). Two approaches were used to analyze the LC-MS/MS data. Manual annotation of MS/MS spectra was performed by calculating expected m/z values of all RNase T1 di […]

[…] al modifications (e.g. pseudouridines, inosines, methylated nucleosides and so forth), such nucleotides are replaced by their unmodified counterparts, according to the RNA modification table from the MODOMICS database (). The removal of modifications from 3D structures is done by the ModeRNA program (). This step is critical because many bioinformatics methods used for RNA secondary structure pred […]