tRNAscanImport: tRNAscanImport: Importing tRNAscan-SE output as GRanges
In FelixErnst/tRNAscanImport: Importing a tRNAscan-SE result file as GRanges object
tRNAscanImport R Documentation
tRNAscanImport: Importing tRNAscan-SE output as GRanges
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.
FelixErnst/tRNAscanImport documentation built on March 29, 2024, 5:44 p.m.
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| tRNAscanImport | R Documentation |
tRNAscanImport: Importing tRNAscan-SE output as GRanges
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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