Man page - gt-ltrdigest(1)
Packages contains this manual
- gt-readjoiner(1)
- gt-cds(1)
- gt-extractfeat(1)
- gt-dupfeat(1)
- gt-select(1)
- gt-encseq(1)
- gt-matstat(1)
- gt-md5_to_id(1)
- gt-seqmutate(1)
- gt-seqtranslate(1)
- gt-mkfeatureindex(1)
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- gt-compreads-refcompress(1)
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- gt-prebwt(1)
- gt-extractseq(1)
- gt-encseq2spm(1)
- gt-convertseq(1)
- gt-clean(1)
- gt-encseq-encode(1)
- gt-ltrclustering(1)
- gt-seq(1)
- gt-ltrharvest(1)
- gt-sequniq(1)
- gt-inlineseq_split(1)
- gt-mergefeat(1)
- gt-splitfasta(1)
- gt-gtf_to_gff3(1)
- gt-ltrdigest(1)
- gt-seqfilter(1)
- gt-featureindex(1)
- gt-inlineseq_add(1)
- gt-speck(1)
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- gt-tallymer-mkindex(1)
- gt-seed_extend(1)
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- gt-sketch(1)
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- gt-seqids(1)
- gt-readjoiner-assembly(1)
- gt-tirvish(1)
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- gt-encseq-sample(1)
- gt-chseqids(1)
- gt-compreads-compress(1)
- gt-scriptfilter(1)
- gt-seqtransform(1)
- gt-eval(1)
- gt-genomediff(1)
- gt-congruence(1)
- gt-chain2dim(1)
- gt-tallymer(1)
- gt-tagerator(1)
- gt-loccheck(1)
- gt-encseq-info(1)
- gt-snpper(1)
- gt-bed_to_gff3(1)
- gt(1)
- gt-matchtool(1)
- gt-simreads(1)
- gt-csa(1)
- gt-tallymer-occratio(1)
- gt-encseq-check(1)
- gt-tallymer-search(1)
- gt-encseq-bench(1)
- gt-shredder(1)
- gt-gff3_to_gtf(1)
- gt-orffinder(1)
- gt-encseq-decode(1)
- gt-compreads(1)
- gt-encseq-md5(1)
- gt-uniq(1)
- gt-congruence-spacedseed(1)
- gt-id_to_md5(1)
- gt-seqorder(1)
- gt-compreads-refdecompress(1)
- gt-fingerprint(1)
- gt-fastq_sample(1)
- gt-interfeat(1)
apt-get install genometools
Manual
GT-LTRDIGEST
NAMESYNOPSIS
DESCRIPTION
REPORTING BUGS
NAME
gt-ltrdigest - Identifies and annotates sequence features in LTR retrotransposon candidates.
SYNOPSIS
gt ltrdigest [option ...] gff3_file
DESCRIPTION
-outfileprefix [ string ]
prefix for output files (e.g. foo will create files called foo_*.csv and foo_*.fas ) Omit this option for GFF3 output only.
-metadata [ yes|no ]
output metadata (run conditions) to separate file (default: yes)
-seqnamelen [ value ]
set maximal length of sequence names in FASTA headers (e.g. for clustalw or similar tools) (default: 20)
-pptlen [ start end ]
required PPT length range (default: [8..30])
-uboxlen [ start end ]
required U-box length range (default: [3..30])
-uboxdist [ value ]
allowed U-box distance range from PPT (default: 0)
-pptradius [ value ]
radius around beginning of 3' LTR to search for PPT (default: 30)
-pptrprob [ value ]
purine emission probability inside PPT (default: 0.970000)
-pptyprob [ value ]
pyrimidine emission probability inside PPT (default: 0.030000)
-pptgprob [ value ]
background G emission probability outside PPT (default: 0.250000)
-pptcprob [ value ]
background C emission probability outside PPT (default: 0.250000)
-pptaprob [ value ]
background A emission probability outside PPT (default: 0.250000)
-ppttprob [ value ]
background T emission probability outside PPT (default: 0.250000)
-pptuprob [ value ]
U/T emission probability inside U-box (default: 0.910000)
-trnas [ filename ]
tRNA library in multiple FASTA format for PBS detection Omit this option to disable PBS search.
-pbsalilen [ start end ]
required PBS/tRNA alignment length range (default: [11..30])
-pbsoffset [ start end ]
allowed PBS offset from LTR boundary range (default: [0..5])
-pbstrnaoffset [ start end ]
allowed PBS/tRNA 3' end alignment offset range (default: [0..5])
-pbsmaxedist [ value ]
maximal allowed PBS/tRNA alignment unit edit distance (default: 1)
-pbsradius [ value ]
radius around end of 5' LTR to search for PBS (default: 30)
-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: NONE)
-aliout [ yes|no ]
output pHMM to amino acid sequence alignments (default: no)
-aaout [ yes|no ]
output amino acid sequences for protein domain hits (default: no)
-allchains [ yes|no ]
output features from all chains and unchained features, labeled with chain numbers (default: no)
-maxgaplen [ value ]
maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits for a protein domain (default: 50)
-force_recreate [ yes|no ]
force recreation of hmmpressed profiles (default: no)
-pbsmatchscore [ value ]
match score for PBS/tRNA alignments (default: 5)
-pbsmismatchscore [ value ]
mismatch score for PBS/tRNA alignments (default: -10)
-pbsinsertionscore [ value ]
insertion score for PBS/tRNA alignments (default: -20)
-pbsdeletionscore [ value ]
deletion score for PBS/tRNA alignments (default: -20)
-v [ yes|no ]
be verbose (default: no)
-o [ filename ]
redirect output to specified file (default: undefined)
-gzip [ yes|no ]
write gzip compressed output file (default: no)
-bzip2 [ yes|no ]
write bzip2 compressed output file (default: no)
-force [ yes|no ]
force writing to output file (default: no)
-seqfile [ filename ]
set the sequence file from which to take the sequences (default: undefined)
-encseq [ filename ]
set the encoded sequence indexname from which to take the sequences (default: undefined)
-seqfiles
set the sequence files from which to extract the features use -- to terminate the list of sequence files
-matchdesc [ yes|no ]
search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)
-matchdescstart [ yes|no ]
exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)
-usedesc [ yes|no ]
use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. If a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID ( III ) and the first range position as offset ( 1000001 ) (default: no)
-regionmapping [ string ]
set file containing sequence-region to sequence file mapping (default: undefined)
-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.