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>.