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>.