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

[Jean lobry]

Dear Sourav Roy Choudhury,

The first thing to do is to check that you have access to data.
Complete virus genomes are in the refseqVirus bank. Try this:

###
  library(seqinr)
  choosebank("refseqViruses")
  query("herp", "TID=548681")
  mnemo <- getName(herp)
  mnemo
  [1] "NC_000898" "NC_001347" "NC_001348" "NC_001350" "NC_001491"
  [6] "NC_001493" "NC_001650" "NC_001664" "NC_001716" "NC_001798"
[11] "NC_001806" "NC_001826" "NC_001844" "NC_001847" "NC_001987"
[16] "NC_002229" "NC_002512" "NC_002531" "NC_002577" "NC_002641"
[21] "NC_002665" "NC_002686" "NC_002794" "NC_003401" "NC_003409"
[26] "NC_003521" "NC_004065" "NC_004367" "NC_004812" "NC_005261"
[31] "NC_005264" "NC_005881" "NC_006146" "NC_006150" "NC_006151"
[36] "NC_006273" "NC_006560" "NC_006623" "NC_007016" "NC_007605"
[41] "NC_007646" "NC_007653" "NC_008210" "NC_008211" "NC_009127"
[46] "NC_009333" "NC_009334" "NC_011587" "NC_011644"
###

Can You reproduce this?

Are those the genomes You want to work with?

Do You want to consider all CDS as a statististical observation
or do You want to consider all genomes as a statistical observation?

Best,

-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
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