GenomeTools - manual page for GT-ORFFINDER(1)

## NAME

gt-orffinder - Identifies ORFs (open reading frames) in sequences.

## SYNOPSIS

gt orffinder [option …] [indexname] [GFF3_file …]

## DESCRIPTION

-types

  Specify regions which should be searched for open reading frames, e.g. LTR_retrotransposon

-allorfs [yes|no]

  search for all ORFs instead of only the longest (default: no)

-min [value]

  minimum length of ORF (default: 30)

-max [value]

  maximum length of ORF (default: 10000)

-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 and exit

-version

  display version information and exit

## REPORTING BUGS

Report bugs to <gt-users@genometools.org>.