Compseq error

[Gary Williams, Tel 01223 494522]

The default action with nucleic acid sequences is to do the composition
analysis on both the forward and the reverse sense.

This action was requested by a user when the program was first being
written.

In the case that you have, with a word size of 1, this does indeed give
very strange-looking results where A = T and C = G.

Try using 'compseq -noreverse' if you wish to only look at the forward
sense.

Gary 

Sabino Liuni wrote:
> 
> Hello everybody
> 
> I have received this information from our user about the Compseq program.
> Any suggestion
> 
> Regards,
> 
> sabino Liuni
> 
> ---------------------------------
> I have noticed that the EMBOSS program COMPSEQ calculates incorrectly w-mer
> nucleotide frequencies. For example the result obtained asking for mononuc
> composition is like the following:
> Total count 2846880
> #
> #       Word Obs Count   Obs Frequency  Exp Frequency   Obs/Exp Frequency
> #
> A       968947              0.3403540                  0.2500000
> 1.3614160
> C        454493                  0.1596460                  0.2500000
>   0.6385840
> G        454493                 0.1596460                   0.2500000
>   0.6385840
> T        968947                 0.3403540                   0.2500000
>    1.3614160
> 
> It seems sum up A+T and C+G.
> -----------------------------------------------------------------

-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK