Under the definition of MAPQ used by Bowtie2, this represents reads with >90% probability of the correct mapping. Reproducibility between biological replicate samples was excellent with Pearson’s R2 = 0.9999. Read length analysis revealed that while shorter reads are less likely to have a ...
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...
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 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 ...