Provided by: genometools_1.5.1-2ubuntu1_amd64 bug


       gt-ltrdigest - Identifies and annotates sequence features in LTR retrotransposon


       gt ltrdigest [option ...] gff3_file indexname


           prefix for output files (e.g.  foo will create files called foo_*.csv and foo_*.fas)
           Omit this option for GFF3 output only.

           set maximal length of sequence names in FASTA headers (e.g. for clustalw or similar
           tools) (default: 20)

           required PPT length range (default: 8 30)

           required U-box length range (default: 3 30)

           allowed U-box distance range from PPT (default: 0)

           radius around beginning of 3' LTR to search for PPT (default: 30)

           tRNA library in multiple FASTA format for PBS detection Omit this option to disable
           PBS search.

           required PBS/tRNA alignment length range (default: 11 30)

           allowed PBS offset from LTR boundary range (default: 0 5)

           allowed PBS/tRNA 3' end alignment offset range (default: 0 5)

           maximal allowed PBS/tRNA alignment unit edit distance (default: 1)

           radius around end of 5' LTR to search for PBS (default: 30)

           be verbose (default: no)

           redirect output to specified file (default: undefined)

           write gzip compressed output file (default: no)

           write bzip2 compressed output file (default: no)

           force writing to output file (default: no)

           display help for basic options and exit

           display help for all options and exit

           display version information and exit


       Report bugs to <>.

                                            10/07/2012                            GT-LTRDIGEST(1)