gt-orffinder - Online in the Cloud

PROGRAM:

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>.

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