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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].