[Seqinr-forum] Query regarding running "Online Synonymous Codon Usage Analyses with the ade4 and seqinR packages"

[Jean lobry]

>  The code is running fine and the codon count table is
>  generated.

Progress bar went to the end?

>  But the problem seems to be that it only produces codon
>  table for the first virus on the list, NC_000898 and not for
>  all the available viruses. Another concern is that for the
>  virus NC_000898 have 104 CDS but it seems to be only 6 CDS
>  is selected here, is it so?

A simple way to check this is:

######
load("tabcod.RData")
sum(tabcod)
[1] 2207194
######

You should have a total of 2,207,194 codons in this dataset, is
it so?

>  Additionally  I do not want to
>  include "Met", "Trp" and "Stop" Codons for
>  the correspondence analysis.
>
>  A minor addition, I want to select only those CDS with
>  length >150 bp or >50 Codons.

This is not a problem, it's easy to do this under R. But first
we should make sure you have the whole data.

Best,

Jean
-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
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