Copy Number Quantification of predicted LTRs (solo LTR prediction)

Detect solo LTR copies and genomic locations of predicted LTR transposons using a BLAST search strategy.

ltr.cn(
  data.sheet,
  LTR.fasta_3ltr,
  LTR.fasta_5ltr,
  genome,
  ltr.similarity = 70,
  scope.cutoff = 0.85,
  perc.ident.cutoff = 70,
  output = NULL,
  max.hits = 500,
  eval = 1e-10,
  cores = 1
)

Arguments

data.sheet	path to the `*_LTRpred_DataSheet.csv` file generated by `LTRpred`.
LTR.fasta_3ltr	path to fasta file storing sequences of 3 prime LTRs generated by `LTRpred`.
LTR.fasta_5ltr	path to fasta file storing sequences of 5 prime LTRs generated by `LTRpred`.
genome	file path to the reference genome in which solo LTRs shall be found (in `fasta` format).
ltr.similarity	similarity threshold for defining LTR similarity.
scope.cutoff	similarity threshold for the scope variable. The scope of a BLAST hit is defined by `abs(s_len - alig_length) / s_len` and aims to quantify the scope ('length similarity between hit and query') of the alignment. Default is `scope.cutoff = 0.85` meaning that at least 85% of the length of the query sequence must match with the length of the subject sequence.
perc.ident.cutoff	choose the minimum sequence identity between the query sequence and subject hit sequence that have a scope >= `scope.cutoff` (e.g. 0.85). Default is `perc.ident.cutoff = 70`. This threshold aims to detect BLAST hits that have similar sequence lengths (controlled by the `scope.cutoff` variable; e.g. `scope.cutoff = 0.85`) and within this scope at least e.g. 70% sequence identity (controlled by the `perc.ident.cutoff` variable).
output	file name of the BLAST output. If `output = NULL` (default) then the BLAST output file will be deleted after the result `data.frame` is returned by this function.
max.hits	maximum number of hits that shall be retrieved that still fulfill the e-value criterium. Default is `max.hits = 65000`.
eval	e-value threshold for BLAST hit detection. Default is `eval = 1E-10`.
cores	number of cores for parallel computations.

References

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.

Gish, W. & States, D.J. (1993) "Identification of protein coding regions by database similarity search." Nature Genet. 3:266-272.

Madden, T.L., Tatusov, R.L. & Zhang, J. (1996) "Applications of network BLAST server" Meth. Enzymol. 266:131-141.

Altschul, S.F., Madden, T.L., Schaeffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402.

Zhang Z., Schwartz S., Wagner L., & Miller W. (2000), "A greedy algorithm for aligning DNA sequences" J Comput Biol 2000; 7(1-2):203-14.

Author

Hajk-Georg Drost