TESTCODE

[Fernan Aguero]

+----[ Matt Berriman <mb4 at sanger.ac.uk> (18.Feb.2003 10:36):
|
| Hi  

Hi Matt,

| can yopu please tell me, what is the EMBOSS equivalent of GCG's TESTCODE?
| thanks
| Matt

When I needed it I didn't find anything like this in EMBOSS,
but I don't know if this functionality has been included in
recent versions of EMBOSS.

The testcode algorithm has been published by Fickett(1) and
Paul Stothard has a Javascript version in his 'Sequence
Manipulation Suite'(2). I've ported Paul's version to perl
and used it succesfully. 

However, please note that I don't have access to GCG and
can't tell if GCG's testcode produce identical results as
the javascript or perl versions.  (it could be possible that
GCG has modified testcode after the original implementation
of the Fickett algorithm). This should not be unexpected since
the cutoff values to decide between coding and non-coding
sequences are hard-coded in testcode and have been derived
by Fickett based on a sample data set from 1982. 

Hope this helps,

Fernan

PD: I can send you the perl testcode if you want it.

1. Recognition of protein coding regions in DNA sequences.
Fickett, JW (1982) Nucleic Acids Res 10(17): 5303

2. The sequence manipulation suite: JavaScript programs for
analyzing and formatting protein and DNA sequences. 
Stothard, P (2000) BioTechniques 28: 1102

| 
| -- 
| 
|  Dr Matthew Berriman 
|  Senior Computer Biologist - Pathogen Sequencing Unit - 
|  The Wellcome Trust Sanger Institute
|  Tel +44 (0)1223 494817 -  Fax +44 (0)1223 494919 
|  http://www.sanger.ac.uk
|
+----]

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan