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gt-tirvish - Online in the Cloud

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This is the command gt-tirvish that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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>.

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