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Name

GETORF

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Status The current release has 0 entries and was indexed 10-Sep-2004.
Creation date 2000 - written - Gary Williams

November 2002 - added indication of reverse sense ORFs

November 2002 - added indication of ORFs that cross the breakpoint atposition 1 in circular genomes.

Description GETORF application details page

Finds and extracts open reading frames (ORFs)

This program finds and outputs the sequences of open reading frames(ORFs).

The ORFs can be defined as regions of a specified minimum size betweenSTOP codons or between START and STOP codons.

The ORFs can be output as the nucleotide sequence or as the translation.

The program can also output the region around the START or the initialSTOP codon or the ending STOP codons of an ORF for those doing analysisof the properties of these regions.

The START and STOP codons are defined in the Genetic Code tables.A suitable Genetic Code table can be selected for the organism you areinvestigating.

Literature None.
WWW www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/getorf.html
Ftp The latest version of the EMBOSS package is available on ftp://ftp.uk.embnet.org/pub/EMBOSS/
Contact This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)
See also
CHECKTRANS Reports STOP codons and ORF statistics of a protein
MARSCAN Finds MAR/SAR sites in nucleic sequences
PLOTORF Plot potential open reading frames
SHOWORF Pretty output of DNA translations
SIXPACK Display a DNA sequence in both direction with its translation
WOBBLE Wobble base plot
Data-fields in SRS
Field Name
Short Name
Type
No. of Keys
No. of Entry References
Indexing Date
Status
ID id id 0 0   not indexed
JobName jnm index 0 0   not indexed
Loaders
EMBOSSDNASIMPLESEQ
EMBOSSPROTSIMPLESEQ
SRS Description Structure ( srsgen.i , srsdb.i , href.i )
Syntax
Information
SRS Release 7.1.3    Copyright © 1997-2003 LION bioscience AG. All Rights Reserved. Terms of Use Feedback