Open Reading Frame Prediction

Source: R/ORFpred.R

This function provides a wrapper to the USEARCH fastx_findorfs command line tool to predict ORFs in a given input fasta file and read the output as data.frame object.

ORFpred(
  seq.file,
  orf.style = 7,
  min.codons = 200,
  trans.seqs = FALSE,
  output = NULL
)

Arguments

seq.file

a fasta file storing the sequences for which open reading frames shall be predicted.
orf.style

type of predicting open reading frames (see documentation of USEARCH).
min.codons

minimum number of codons in the predicted open reading frame.
trans.seqs

logical value indicating wheter or not predicted open reading frames shall be translated and the corresponding protein sequences stored in the output folder.
output

path to the folder in which predicted open reading frame sequences shall be stored.

References

Robert Edgar. Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 26 (19): 2460-2461.

See also

LTRharvest, LTRdigest, LTRpred

Author

Hajk-Georg Drost