<div dir="ltr"><div>(Question at the end of the e-mail)</div><div><br></div><div>Hi Jean,</div><div><br></div><div>After asking for help in several places, I got the following reply from a very helpful member of this database:</div>
<div><a href="http://gtrnadb.ucsc.edu/">http://gtrnadb.ucsc.edu/</a></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">She wrote to me that:</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
Primary sequences of different tRNA isotypes do not align well. You will have to include the secondary structure to do the alignments. The secondary structure page of each genome in GtRNAdb shows the linear representation of the secondary structure for each tRNA produced with covariance model. You can use that to align the tRNAs you are interested.</blockquote>
<blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
<br></blockquote><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
Hope this help.</blockquote><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
Patricia</blockquote></span></div><div><br></div><div>Now, for our example, if I want to have this:</div><div><a href="http://gtrnadb.ucsc.edu/Aero_pern/Aero_pern-align.html">http://gtrnadb.ucsc.edu/Aero_pern/Aero_pern-align.html</a></div>
<div>Imported into R, I could try to use a file from here:</div><div><a href="http://gtrnadb.ucsc.edu/Aero_pern/Aero_pern-structs.html">http://gtrnadb.ucsc.edu/Aero_pern/Aero_pern-structs.html</a></div><div>(Which is based on a calculation of the secondary structure of the tRNA)</div>
<div>If I had that file easily available that would be nice. But I can't seem to download it from the site.</div><div><br></div><div>Which leaves me asking:</div><div>1) Should I (somehow) compute the secondary structures of tRNA's, and then use that for alignment ?</div>
<div>2) (if yes) How can I compute the secondary structures of tRNA's in R? (is it even possible?!)</div><div>3) After doing that, is there a tool to easily align the tRNA's ? (in the dataset I gave links to there is a <a href="http://gtrnadb.ucsc.edu/legend.html">legend </a>of how to do this with that algorithm coding. But I imagine this will be different for each coding system)</div>
<div><br></div><div><br></div><div>Thanks for any help,</div><div>Tal</div><div><br></div><div><br></div><br clear="all"><br>----------------Contact Details:-------------------------------------------------------<br>Contact me: <a href="mailto:Tal.Galili@gmail.com">Tal.Galili@gmail.com</a> | 972-52-7275845<br>
Read me: <a href="http://www.talgalili.com">www.talgalili.com</a> (Hebrew) | <a href="http://www.biostatistics.co.il">www.biostatistics.co.il</a> (Hebrew) | <a href="http://www.r-statistics.com">www.r-statistics.com</a> (English)<br>
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<br><br><div class="gmail_quote">On Sat, Mar 13, 2010 at 8:06 PM, 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;">
<div class="im">At 23:03 +0200 11/03/10, Tal Galili wrote:<br>
Hello dear list.<br>
<br>
I wish (for my thesis work), to import tRNA data into R and have it aligned.<br>
<br>
My questions are:<br>
1) What resources can I use for the data.<br>
2) What commands might help me with the import/alignment.<br>
<br>
<br>
So far, I found two nice repositories that holds such data:<br>
<br></div>
1) <<<a href="http://trnadb.bioinf.uni-leipzig.de/Result" target="_blank">http://trnadb.bioinf.uni-leipzig.de/Result</a>><a href="http://trnadb.bioinf.uni-leipzig.de/Result" target="_blank">http://trnadb.bioinf.uni-leipzig.de/Result</a>><<a href="http://trnadb.bioinf.uni-leipzig.de/Result" target="_blank">http://trnadb.bioinf.uni-leipzig.de/Result</a>><a href="http://trnadb.bioinf.uni-leipzig.de/Result" target="_blank">http://trnadb.bioinf.uni-leipzig.de/Result</a><br>
2) <<<a href="http://gtrnadb.ucsc.edu/download.html" target="_blank">http://gtrnadb.ucsc.edu/download.html</a>><a href="http://gtrnadb.ucsc.edu/download.html" target="_blank">http://gtrnadb.ucsc.edu/download.html</a>><<a href="http://gtrnadb.ucsc.edu/download.html" target="_blank">http://gtrnadb.ucsc.edu/download.html</a>><a href="http://gtrnadb.ucsc.edu/download.html" target="_blank">http://gtrnadb.ucsc.edu/download.html</a><div class="im">
<br>
<br>
And also the readFASTA command from Biostrings, that does basic importing of the data into R.<br>
<br>
My problem still remains with how to handle the alignment of the tRNA.<br>
<br>
Since I am not from the field, I might be missing a very basic answer (like where I should download the data from, or what command to use).<br>
If you might be willing to advice me, that would be most helpful.<br>
<br>
Many thanks in advance,<br>
Tal<br>
<br></div>
Hi Tal,<br>
<br>
let's start from <a href="http://trnadb.bioinf.uni-leipzig.de/Search" target="_blank">http://trnadb.bioinf.uni-leipzig.de/Search</a> which is<br>
a nice ressource and suppose that you are interested in Ala tRNA.<br>
<br>
Select the Alanine checkbox and then click on the "search database"<br>
button. Wait for the search result page. At the bottom, select<br>
the "select all sequences of search" checkbox, on the scrolling<br>
menu just on the right select the "send alignment (multiFASTA)"<br>
and then click on the "submit" button. A file called "fasta.mfa"<br>
should be downloaded on your computer.<br>
<br>
Then under R:<br>
<br>
###<br>
library(seqinr)<br>
res <- read.alignment(file.choose(), format = "fasta")<br>
names(res)<br>
[1] "nb" "nam" "seq" "com"<br>
res$nb<br>
[1] 605<br>
###<br>
<br>
The alignment of 605 tRNA sequences has been imported in the<br>
object called "res", now you can play with it. For instance<br>
the consensus with the majority rule is:<br>
<br>
###<br>
consensus(res)<br>
[1] "-" "g" "g" "g" "g" "c" "t" "g" "t" "a" "g" "c" "t" "c"<br>
[15] "a" "g" "c" "t" "-" "g" "g" "t" "-" "-" "a" "g" "a" "g"<br>
[29] "c" "g" "c" "c" "t" "g" "c" "t" "t" "t" "g" "c" "a" "t"<br>
[43] "g" "c" "a" "g" "g" "a" "g" "-" "g" "t" "c" "a" "g" "g"<br>
[57] "g" "g" "t" "t" "c" "g" "a" "t" "c" "c" "c" "c" "c" "t"<br>
[71] "c" "a" "g" "c" "t" "c" "c" "a" "-" "-" "-"<br>
###<br>
<br>
HTH,<br>
<br>
Z.<br><font color="#888888">
<br>
<br>
-- <br>
Pr. Jean R. Lobry (Dr. phil. hab.)<br>
Head of Laboratoire de Police Scientifique de Lyon<br>
Institut National de Police Scientifique<br>
31 av. F. Roosevelt, F-69134 ECULLY CEDEX<br>
Allo: +33 (0)4 72 86 89 60<br>
e-mail: <a href="mailto:jean.lobry@interieur.gouv.fr" target="_blank">jean.lobry@interieur.gouv.fr</a><br>
<br>
<br>
</font></blockquote></div><br></div>