<div>Dear Dr. L<span class="Apple-style-span" style="font-family: arial, sans-serif, 'Arial Unicode MS'; font-size: 13px; border-collapse: collapse; white-space: pre-wrap; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; ">obry and <span class="Apple-style-span" style="font-family: arial, helvetica, clean, sans-serif; white-space: normal; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; line-height: 15px; ">Colleagues,</span></span></div>
<div><font class="Apple-style-span" face="arial, helvetica, clean, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; line-height: 15px;"><br></span></font></div><div><font class="Apple-style-span" face="arial, helvetica, clean, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; line-height: 15px;">The code is running fine and I can reproduce the output as same as yours. It seems that the data is accessible. </span></font></div>
<div><font class="Apple-style-span" face="arial, helvetica, clean, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; line-height: 15px;"><br></span></font></div><div><font class="Apple-style-span" face="arial, helvetica, clean, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; line-height: 15px;">Yes, these are absolutely those genomes that I intend to work with. I want <span class="Apple-style-span" style="border-collapse: separate; font-family: arial; line-height: normal; ">to consider only all the CDS (or Open Reading Frame) for the statistical observation.</span></span></font></div>
<div><br></div><div>Thank you very much</div><div><br></div><div>Sincerely yours</div><div>Sourav Roy Choudhury</div><div><br></div><div><span class="Apple-style-span" style="font-family: arial, helvetica, clean, sans-serif; font-size: 13px; border-collapse: collapse; color: rgb(136, 136, 136); line-height: 15px; ">SOURAV ROY CHOUDHURY.<br style="line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">
Dept of Neuroscience<br style="line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">University of Calcutta <br style="line-height: 1.2em; outline-style: none; outline-width: initial; outline-color: initial; ">
West Bengal, INDIA</span></div><div><br></div><br><br><div><br></div><div><br><div class="gmail_quote">On Wed, Nov 4, 2009 at 12:12 AM, Jean lobry <span dir="ltr"><<a href="mailto:lobry@biomserv.univ-lyon1.fr">lobry@biomserv.univ-lyon1.fr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dear Sourav Roy Choudhury,<br>
<br>
The first thing to do is to check that you have access to data.<br>
Complete virus genomes are in the refseqVirus bank. Try this:<br>
<br>
###<br>
library(seqinr)<br>
choosebank("refseqViruses")<br>
query("herp", "TID=548681")<br>
mnemo <- getName(herp)<br>
mnemo<br>
[1] "NC_000898" "NC_001347" "NC_001348" "NC_001350" "NC_001491"<br>
[6] "NC_001493" "NC_001650" "NC_001664" "NC_001716" "NC_001798"<br>
[11] "NC_001806" "NC_001826" "NC_001844" "NC_001847" "NC_001987"<br>
[16] "NC_002229" "NC_002512" "NC_002531" "NC_002577" "NC_002641"<br>
[21] "NC_002665" "NC_002686" "NC_002794" "NC_003401" "NC_003409"<br>
[26] "NC_003521" "NC_004065" "NC_004367" "NC_004812" "NC_005261"<br>
[31] "NC_005264" "NC_005881" "NC_006146" "NC_006150" "NC_006151"<br>
[36] "NC_006273" "NC_006560" "NC_006623" "NC_007016" "NC_007605"<br>
[41] "NC_007646" "NC_007653" "NC_008210" "NC_008211" "NC_009127"<br>
[46] "NC_009333" "NC_009334" "NC_011587" "NC_011644"<br>
###<br>
<br>
Can You reproduce this?<br>
<br>
Are those the genomes You want to work with?<br>
<br>
Do You want to consider all CDS as a statististical observation<br>
or do You want to consider all genomes as a statistical observation?<br>
<br>
Best,<br><font color="#888888">
<br>
-- <br>
Jean R. Lobry (<a href="mailto:lobry@biomserv.univ-lyon1.fr" target="_blank">lobry@biomserv.univ-lyon1.fr</a>)<br>
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,<br>
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE<br>
allo : +33 472 43 27 56 fax : +33 472 43 13 88<br>
<a href="http://pbil.univ-lyon1.fr/members/lobry/" target="_blank">http://pbil.univ-lyon1.fr/members/lobry/</a><br>
<br>
<br>
</font></blockquote></div><br></div>