gt-orffinder1
Identifies orfs (open reading frames) in sequences.
Usage
gt orffinder
[option ...]
[indexname]
[GFF3_file ...]
Overview
-
-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
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.