gt-tirvish1
Identify terminal inverted repeat (tir) elements,such as dna transposons.
Usage
gt tirvish
[option ...]
-index
INDEXNAME
Overview
-
-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
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.
-md5 since Debian 9 (Stretch);
-refseqs since Debian 9 (Stretch);
-seqids since Debian 9 (Stretch).