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gt-orffinder - Online in the Cloud

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This is the command gt-orffinder that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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 <[email protected]>.

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