Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA popul...
This need for improved resolution provided the impetus to standardize high-throughput sequencing methodologies capable of discerning tRNA genes at the isodecoder level. Next-generation RNA sequencing has revolutionized modern molecular biology for most types of transcripts, except tRNAs. Historically, tRNAs ...
A different assembly or tRNA space definition is used. The lookup table can be built with various species/assemblies. If GRCh37 is desired with the tRNA space as described in the text, then Supplementary Table 1 can be used. The number of candidate Not all post-transcriptional Perform ...
However, the recognition of glycine, which has no side chain, is limited by definition and thus the fingerprinting approach might fail to capture subtle recognition features. AspRSs and AsnRSs are located next to each other in the embedding space. Their recognition mechanisms seem to be very ...
Central to identifying tRFs among the transcripts of a tissue or cell of interest is the definition of the reference tRNA space, i.e. the union of genomic locations that harbor the DNA templates of tRNAs. In order to define the tRNA space, we need a comprehensive collection of tRNA genes ...
While the definition of Q seems convoluted, it has been constructed as a metric whose value reflects the degree of amino acid diversity generated by typical evolutionary amino acid substitution processes, reflected in the substitution matrix that it uses as a reference. Different matrices do not ...
While defining modules in biology can be challenging, the fact that modules must be "evolutionary units" enables the use of phylogenetic methods to appropriately test definitions of modularity. In this regard and in the absence of clear statements of topographic correspondence, definition of modules ...
The latter definition of distance in NNN is similar to the one used for the definition of the Hamming distance in a hypercube (ℤ2)n, where the only scalars are zero and one. The Manhattan distance gives us the minimal number of edges or unitary segments in a path between two triplets...