NAME

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

SYNOPSIS

       gt ltrdigest [option ...] gff3_file indexname

OPTIONS

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

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

       -pptlen
           required PPT length range (default: 8 30)

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

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

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

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

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

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

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

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

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

       -v
           be verbose (default: no)

       -o
           redirect output to specified file (default: undefined)

       -gzip
           write gzip compressed output file (default: no)

       -bzip2
           write bzip2 compressed output file (default: no)

       -force
           force writing to output file (default: no)

       -help
           display help for basic options and exit

       -help+
           display help for all options and exit

       -version
           display version information and exit

AUTHOR

       Report bugs to <gt-users@genometools.org>.

                                                   10/07/2012                                    GT-LTRDIGEST(1)