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PROGRAM:

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 <gt-users@genometools.org>.

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