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GT-TIRVISH(1) GenomeTools Manual GT-TIRVISH(1)

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: 27)
-maxtirlen [value]
specify maximum length for each TIR (default: 1000)
-mintirdist [value]
specify minimum distance of TIRs (default: 100)
-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 similaritythreshold in range [1..100%] (default: 85.000000)
-overlaps [...]
specify no|best|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 (default: 0.000001)
-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)
-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>.
09/05/2014 GenomeTools 1.5.3