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 |