version 1.0.2

**Zhao XU and Hao WANG**

- 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*

- -o,
- Acknowledgements
- Bibliography
- About this document ...

2009-04-09