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Table 1 Parameter sets for LTRharvest used for predictions in genomes of S. cerevisiae and D. melanogaster

From: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

Parameter name Default Value S. cer. Value D. mel. Comment
seed 30 100 76 exact match length requirement for 5'-3' LTR pair
minlenltr 100 100 116 length constraint for 5'-3' LTR pair, in bp
maxlenltr 1000 1000 800 length constraint for 5'-3' LTR pair, in bp
mindistltr 1000 1500 2280 distance constraint for 5'-3' LTR pair, in bp
maxdistltr 15000 15000 8773 distance constraint for 5'-3' LTR pair, in bp
similar 85% 80.0% 91.0% similarity threshold of a 5'-3' LTR pair, in bp
xdrop 5 5 7 Xdrop score for extending seed
mat 2 2 2 match score
mis -2 -2 -2 mismatch score
ins -3 -3 -3 insertion score
del -3 -3 -3 deletion score
mintsd 4 5 4 minimal length of a target site duplication (TSD), in bp
maxtsd 20 20 20 maximal length of a target site duplication (TSD), in bp
motif - tg...ca - required motif
motifmis 0 0 0 maximum number of mismatches in motif
vic 60 60 60 number of nucleotide positions (vicinity) to the left and to the right, respectively, for searching TSD and motif around boundaries
overlaps best best best strategy for handling predicted LTR elements which overlap
  1. column 'value S. cer.' = setting for S. cerevisiae
  2. column 'value D. mel.' = setting for D. melanogaster
  3. For a detailed description of parameters, see the manual of LTRharvest [33].