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Name

PLOTORF

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Status The current release has 0 entries and was indexed 14-Sep-2004.
Creation date Written (1999) - Alan Bleasby
Description PLOTORF application details page

Plot potential open reading frames

Plot potential open reading frames.

A graphical representation of where the open reading frames are in all 6reading frames is shown. The ORFs are displayed as blue boxes.

ORFs in this program are defined as being regions between START and STOPcodons.

Note that this definition of an ORF would miss those exons in eukaryoticgenomic sequences which do not contain a START codon. plotorf isonly really useful when dealing with prokaryotic or mRNA eukaryoticsequences.

The default START codon is: "ATG".
The default STOP codons are: "TAA,TAG,TGA".

You can specify your own set of start and stop codons using the-start and -stop qualifiers.

Literature None.
WWW www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/plotorf.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 Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
See also
BACKTRANSEQ Back translate a protein sequence
GETORF Finds and extracts open reading frames (ORFs)
MARSCAN Finds MAR/SAR sites in nucleic sequences
PRETTYSEQ Output sequence with translated ranges
REMAP Display a sequence with restriction cut sites, translation etc..
SHOWORF Pretty output of DNA translations
SHOWSEQN Display a sequence with features, translation etc..
SIXPACK Display a DNA sequence in both direction with its translation
TRANSEQ Translate nucleic acid sequences
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
PLOTORFLOAD
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