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

[sourav roy choudhury]

Dear Dr. Lobry and Colleagues,

The code is running fine and I can reproduce the output as same as yours. It
seems that the data is accessible.

Yes, these are absolutely those genomes that I intend to work with. I want to
consider only all the CDS (or Open Reading Frame) for
the statistical observation.

Thank you very much

Sincerely yours
Sourav Roy Choudhury

SOURAV ROY CHOUDHURY.
Dept of Neuroscience
University of Calcutta
West Bengal, INDIA





On Wed, Nov 4, 2009 at 12:12 AM, Jean lobry <lobry at biomserv.univ-lyon1.fr>wrote:

> 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
> http://pbil.univ-lyon1.fr/members/lobry/
>
>
>
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