gt-ltrdigest1
Identifies and annotates sequence features in ltr retrotransposon candidates.
Usage
gt ltrdigest
[option ...]
gff3_file
Overview
-
-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
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.
-force_recreate since Debian 9 (Stretch).