tRNAscanImport: tRNAscanImport: Importing tRNAscan-SE output as GRanges

In tRNAscanImport: Importing a tRNAscan-SE result file as GRanges object

Description

tRNAscan-SE can be used for prediction of tRNA genes in whole genomes based on sequence context and calculated structural features. Many tRNA annotations in genomes contain or are based on information generated by tRNAscan-SE, for example the current SGD reference genome sacCer3 for Saccharomyces cerevisiae. However, not all available information from tRNAscan-SE end up in the genome annotation. Among these are for example structural information, additional scores and the information, whether the conserved CCA-end is encoded in the genomic DNA. To work with this complete set of information, the tRNAscan-SE output can be parsed into a more accessible GRanges object using 'tRNAscanImport'.

Manual

Please refer to the tRNAscanImport vignette for an example how to work and use the package: tRNAscanImport

Author(s)

Felix G M Ernst [aut]

References

Chan, Patricia P., and Todd M. Lowe. 2016. “GtRNAdb 2.0: An Expanded Database of Transfer Rna Genes Identified in Complete and Draft Genomes.” Nucleic Acids Research 44 (D1): D184–189.. doi:10.1093/nar/gkv1309.

Lowe, T. M., and S. R. Eddy. 1997. “TRNAscan-Se: A Program for Improved Detection of Transfer Rna Genes in Genomic Sequence.” Nucleic Acids Research 25 (5): 955–964.

tRNAscanImport documentation built on Nov. 8, 2020, 7:48 p.m.