EnglishFrenchSpanish

OnWorks favicon

getorfe - Online in the Cloud

Run getorfe in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command getorfe 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


getorf - Finds and extracts open reading frames (ORFs)

SYNOPSIS


getorf -sequence seqall [-table list] [-minsize integer] [-maxsize integer] [-find list]
-methionine boolean -circular boolean -reverse boolean -flanking integer
-outseq seqoutall

getorf -help

DESCRIPTION


getorf is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Nucleic:Gene finding" command group(s).

OPTIONS


Input section
-sequence seqall

Additional section
-table list

-minsize integer
Default value: 30

-maxsize integer
Default value: 1000000

-find list
This is a small menu of possible output options. The first four options are to select
either the protein translation or the original nucleic acid sequence of the open
reading frame. There are two possible definitions of an open reading frame: it can
either be a region that is free of STOP codons or a region that begins with a START
codon and ends with a STOP codon. The last three options are probably only of interest
to people who wish to investigate the statistical properties of the regions around
potential START or STOP codons. The last option assumes that ORF lengths are
calculated between two STOP codons.

Advanced section
-methionine boolean
START codons at the beginning of protein products will usually code for Methionine,
despite what the codon will code for when it is internal to a protein. This qualifier
sets all such START codons to code for Methionine by default. Default value: Y

-circular boolean
Default value: N

-reverse boolean
Set this to be false if you do not wish to find ORFs in the reverse complement of the
sequence. Default value: Y

-flanking integer
If you have chosen one of the options of the type of sequence to find that gives the
flanking sequence around a STOP or START codon, this allows you to set the number of
nucleotides either side of that codon to output. If the region of flanking nucleotides
crosses the start or end of the sequence, no output is given for this codon. Default
value: 100

Output section
-outseq seqoutall

Use getorfe online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Image Downloader
    Image Downloader
    Crawl and download images using
    Selenium Using python3 and PyQt5.
    Supported Search Engine: Google, Bing,
    Baidu. Keywords input from the keyboard
    or input from ...
    Download Image Downloader
  • 2
    Eclipse Tomcat Plugin
    Eclipse Tomcat Plugin
    The Eclipse Tomcat Plugin provides
    simple integration of a tomcat servlet
    container for the development of java
    web applications. You can join us for
    discussio...
    Download Eclipse Tomcat Plugin
  • 3
    WebTorrent Desktop
    WebTorrent Desktop
    WebTorrent Desktop is for streaming
    torrents on Mac, Windows or Linux. It
    connects to both BitTorrent and
    WebTorrent peers. Now there's no
    need to wait for...
    Download WebTorrent Desktop
  • 4
    GenX
    GenX
    GenX is a scientific program to refine
    x-ray refelcetivity, neutron
    reflectivity and surface x-ray
    diffraction data using the differential
    evolution algorithm....
    Download GenX
  • 5
    pspp4windows
    pspp4windows
    PSPP is a program for statistical
    analysis of sampled data. It is a free
    replacement for the proprietary program
    SPSS. PSPP has both text-based and
    graphical us...
    Download pspp4windows
  • 6
    Git Extensions
    Git Extensions
    Git Extensions is a standalone UI tool
    for managing Git repositories. It also
    integrates with Windows Explorer and
    Microsoft Visual Studio
    (2015/2017/2019). Th...
    Download Git Extensions
  • More »

Linux commands

Ad