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LTR_FINDER USER MANUAL
version 1.0.2
- Algorithm
- Input data
- Output format
- Parameters
- -o, Gap open penalty, (positive integer)
-t, Gap extend penalty, (positive integer)
-e, Gap end penalty, (positive integer)
-m, Match score, (positive integer)
-u, Mismatch score, (negative integer)
- -D, Max distance between LTRs, (positive integer)
-d, Min distance between LTRs, (positive integer)
-L, Max LTR Length, (positive integer)
-l, Min LTR Length, (positive integer)
- -g, Extension max gap, (positive integer)
-j, Extension cutoff, (decimal between 0 and 1)
-J, Reliable extension, (decimal between 0 and 1)
- -p, Length of exact match pairs, (positive integer)
- -r, Min match length for PBS detection, (positive integer)
- -s, Predict PBS by using which tRNA database, (filename)
- -a, Use ps_scan to predict IN(core), IN(c-term) and RH, dirname
- -S, Output score threshold, (integer)
- -B, Sharpness higher threshold, (decimal between 0 and 1)
-b, Sharpness lower threshold, (decimal between 0 and 1)
- -w, Output format, (0,1 or 2)
- -O, Length of alignment details, (positive integer)
- -P, Sequence ID pattern, (POSIX regular expression)
- -F, Signals status control, (01 string)
- -C, Auto mask highly repeated regions
- Acknowledgements
- Bibliography
- About this document ...
2009-04-09