Importing information from the tRNA db as GRanges object

title

TRNA_DB_URL

TRNA_DB_URL_MT

import.tRNAdb.id(
  tdbID,
  database = c("DNA", "RNA"),
  origin = c("allothers", "plastid", "mitochondrial"),
  dbURL = TRNA_DB_URL,
  verbose = FALSE
)

import.mttRNAdb.id(mtdbID, dbURL = TRNA_DB_URL_MT, verbose = FALSE)

import.tRNAdb.blast(
  blastSeq,
  database = c("DNA", "RNA"),
  origin = c("allothers", "plastid", "mitochondrial"),
  dbURL = TRNA_DB_URL,
  verbose = FALSE
)

import.tRNAdb(
  organism = "",
  strain = "",
  taxonomyID = "",
  aminoacids = "",
  anticodons = "",
  sequences = list(),
  structures = list(),
  reference = "",
  comment = "",
  pubmed = "",
  genes = "",
  database = c("DNA", "RNA"),
  origin = c("allothers", "plastid", "mitochondrial"),
  dbURL = TRNA_DB_URL,
  verbose = FALSE
)

import.mttRNAdb(
  organism = "",
  strain = "",
  taxonomyID = "",
  aminoacids = "",
  anticodons = "",
  sequences = list(),
  structures = list(),
  reference = "",
  comment = "",
  pubmed = "",
  genes = "",
  dbURL = TRNA_DB_URL_MT,
  verbose = FALSE
)

tRNAdb2GFF(input)

Format

An object of class character of length 1.

Arguments

tdbID: a tRNAdb ID
database: "RNA" or "DNA"
origin: one ore more of "plastid", "mitochondrial" or "allothers"
dbURL: the URL of the tRNA db
verbose: whether to report verbose information from the httr2 calls
mtdbID: a mtRNAdb ID
blastSeq: a sequence to use for a blast search
organism: a organism name as a character string
strain: a strain information as a character string
taxonomyID: organism and strain information as a taxonom ID
aminoacids: a character vector of amino acids as a three letter code
anticodons: a character vector of anticodon sequences
sequences: a named (1-15) list of sequences, which are used for the search
structures: a named (1-15) list of structures, which are used for the search. Please use the \(\) or >< dot bracket annotation.
reference: a reference as a character string
comment: a comment as a character string
pubmed: a pubmed ID
genes: a gene name as a character string
input: a GRanges object which passes the istRNAdbGRanges check

Value

a GRanges object containing the information from the tRNA db

Examples

import.tRNAdb(organism = "Saccharomyces cerevisiae",
              aminoacids = c("Phe","Ala"))
#> Warning: tRNAdb Server seems to be not available.
#> GRanges object with 0 ranges and 0 metadata columns:
#>    seqnames    ranges strand
#>       <Rle> <IRanges>  <Rle>
#>   -------
#>   seqinfo: no sequences
import.tRNAdb.id(tdbID = "tdbD00000785")
#> Warning: tRNAdb Server seems to be not available.
#> GRanges object with 0 ranges and 0 metadata columns:
#>    seqnames    ranges strand
#>       <Rle> <IRanges>  <Rle>
#>   -------
#>   seqinfo: no sequences
import.tRNAdb.blast(blastSeq =
"GCGGATTTAGCTCAGTTGGGAGAGCGCCAGACTGAAGATCTGGAGGTCCTGTGTTCGATCCACAGAATTCGCA")
#> Warning: tRNAdb Server seems to be not available.
#> GRanges object with 0 ranges and 0 metadata columns:
#>    seqnames    ranges strand
#>       <Rle> <IRanges>  <Rle>
#>   -------
#>   seqinfo: no sequences
import.mttRNAdb(organism = "Bos taurus",
                aminoacids = c("Phe","Ala"))
#> Warning: tRNAdb Server seems to be not available.
#> GRanges object with 0 ranges and 0 metadata columns:
#>    seqnames    ranges strand
#>       <Rle> <IRanges>  <Rle>
#>   -------
#>   seqinfo: no sequences
import.mttRNAdb.id(mtdbID = "mtdbD00000900")
#> Warning: tRNAdb Server seems to be not available.
#> GRanges object with 0 ranges and 0 metadata columns:
#>    seqnames    ranges strand
#>       <Rle> <IRanges>  <Rle>
#>   -------
#>   seqinfo: no sequences