Compseq error
Gary Williams, Tel 01223 494522
gwilliam at hgmp.mrc.ac.uk
Mon Apr 2 15:12:08 UTC 2001
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
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