NAME

       gt-tirvish - Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.

SYNOPSIS

       gt tirvish [option ...] -index INDEXNAME

DESCRIPTION

       -index [string]
           specify the name of the enhanced suffix array index (mandatory) (default: undefined)

       -seed [value]
           specify minimum seed length for exact repeats (default: 20)

       -mintirlen [value]
           specify minimum length for each TIR (default: 100)

       -maxtirlen [value]
           specify maximum length for each TIR (default: 1000)

       -mintirdist [value]
           specify minimum distance of TIRs (default: 500)

       -maxtirdist [value]
           specify maximum distance of TIRs (default: 10000)

       -mat [value]
           specify matchscore for extension-alignment (default: 2)

       -mis [value]
           specify mismatchscore for extension-alignment (default: -2)

       -ins [value]
           specify insertionscore for extension-alignment (default: -3)

       -del [value]
           specify deletionscore for extension-alignment (default: -3)

       -xdrop [value]
           specify xdropbelowscore for extension-alignment (default: 5)

       -similar [value]
           specify TIR similarity threshold in therange [1..100%] (default: 85.000000)

       -overlaps [...]
           specify no|best|longest|all (default: best)

       -mintsd [value]
           specify minimum length for each TSD (default: 2)

       -maxtsd [value]
           specify maximum length for each TSD (default: 11)

       -vic [value]
           specify the number of nucleotides (to the left and to the right) that will be searched
           for TSDs around 5' and 3' boundary of predicted TIRs (default: 60)

       -hmms
           profile HMM models for domain detection (separate by spaces, finish with --) in HMMER3
           format Omit this option to disable pHMM search.

       -pdomevalcutoff [value]
           global E-value cutoff for pHMM search default 1E-6

       -pdomcutoff [...]
           model-specific score cutoff choose from TC (trusted cutoff) | GA (gathering cutoff) |
           NONE (no cutoffs) (default: GA)

       -maxgaplen [value]
           maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits
           for a protein domain (default: 50)

       -refseqs [string]
           specify the name of the gene sequences to scan for inside candidates (default:
           undefined)

       -seqids [yes|no]
           use sequence descriptions instead of sequence numbers in GFF3 output (default: yes)

       -md5 [yes|no]
           add MD5 hashes to seqids in GFF3 output (default: no)

       -help
           display help for basic options and exit

       -help+
           display help for all options and exit

       -version
           display version information and exit

REPORTING BUGS

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