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


gt tirvish [option ...] -index INDEXNAME


-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)

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:

-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)

display help for basic options and exit

display help for all options and exit

display version information and exit


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

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