table of contents
other versions
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- testing 1.6.5+ds-2
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| GT-ORFFINDER(1) | GenomeTools Manual | 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 https://github.com/genometools/genometools/issues.
| 08/17/2021 | GenomeTools 1.6.2 |