Man page - gt-tirvish(1)
Packages contas this manual
- gt-scriptfilter(1)
- gt-mmapandread(1)
- gt-gff3(1)
- gt-ltrdigest(1)
- gt-encseq(1)
- gt-extractfeat(1)
- gt-seed_extend(1)
- gt-dupfeat(1)
- gt-csa(1)
- gt-clean(1)
- gt-packedindex(1)
- gt-genomediff(1)
- gt-sketch_page(1)
- gt-compreads-refcompress(1)
- gt-splicesiteinfo(1)
- gt-extractseq(1)
- gt-compreads(1)
- gt-encseq-decode(1)
- gt-cds(1)
- gt-encseq-bitextract(1)
- gt-readjoiner(1)
- gt-tallymer-occratio(1)
- gt-tallymer(1)
- gt-sequniq(1)
- gt-id_to_md5(1)
- gt-readjoiner-prefilter(1)
- gt-seqtranslate(1)
- gt-tallymer-search(1)
- gt-condenseq(1)
- gt-seqmutate(1)
- gt-seqorder(1)
- gt-seq(1)
- gt-inlineseq_add(1)
- gt-repfind(1)
- gt-seqfilter(1)
- gt-sketch(1)
- gt-hop(1)
- gt-seqids(1)
- gt-fastq_sample(1)
- gt-compreads-refdecompress(1)
- gt-readjoiner-assembly(1)
- gt-readjoiner-overlap(1)
- gt-splitfasta(1)
- gt-seqtransform(1)
- gt-tallymer-mkindex(1)
- gt-wtree(1)
- gt-ltrharvest(1)
- gt-chseqids(1)
- gt-compreads-decompress(1)
- gt-orffinder(1)
- gt-encseq-sample(1)
- gt-encseq-md5(1)
- gt-merge(1)
- gt-gff3validator(1)
- gt-matchtool(1)
- gt-congruence(1)
- gt-tagerator(1)
- gt-gff3_to_gtf(1)
- gt-featureindex(1)
- gt-md5_to_id(1)
- gt-mkfeatureindex(1)
- gt-tirvish(1)
- gt-snpper(1)
- gt-prebwt(1)
- gt-stat(1)
- gt-speck(1)
- gt-convertseq(1)
- gt-compreads-compress(1)
- gt-interfeat(1)
- gt-chain2dim(1)
- gt-encseq-bench(1)
- gt-shulengthdist(1)
- gt-encseq-encode(1)
- gt-select(1)
- gt-uniq(1)
- gt-shredder(1)
- gt-fingerprint(1)
- gt-matstat(1)
- gt-encseq-info(1)
- gt-congruence-spacedseed(1)
- gt-encseq2spm(1)
- gt-simreads(1)
- gt(1)
- gt-dot(1)
- gt-ltrclustering(1)
- gt-seqstat(1)
- gt-mergefeat(1)
- gt-bed_to_gff3(1)
- gt-uniquesub(1)
- gt-gtf_to_gff3(1)
- gt-eval(1)
- gt-encseq-check(1)
- gt-loccheck(1)
- gt-inlineseq_split(1)
Package: genometools
apt-get install genometools
apt-get install genometools
Manuals in package:
Documentations in package:
Manual
| 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: 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 https://github.com/genometools/genometools/issues.
| 04/27/2024 | GenomeTools 1.6.5 |