[Seqinr-forum] How (and where) to get aligned tRNA sequences (and import it into R)

[Tal Galili]

(Question at the end of the e-mail)

Hi Jean,

After asking for help in several places, I got the following reply from a
very helpful member of this database:
http://gtrnadb.ucsc.edu/

She wrote to me that:

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.


> Hope this help.

Patricia


Now, for our example, if I want to have this:
http://gtrnadb.ucsc.edu/Aero_pern/Aero_pern-align.html
Imported into R, I could try to use a file from here:
http://gtrnadb.ucsc.edu/Aero_pern/Aero_pern-structs.html
(Which is based on a calculation of the secondary structure of the tRNA)
If I had that file easily available that would be nice. But I can't seem to
download it from the site.

Which leaves me asking:
1) Should I (somehow) compute the secondary structures of tRNA's, and then
use that for alignment ?
2) (if yes) How can I compute the secondary structures of tRNA's in R? (is
it even possible?!)
3) After doing that, is there a tool to easily align the tRNA's ? (in the
dataset I gave links to there is a legend
<http://gtrnadb.ucsc.edu/legend.html>of how to do this with that algorithm
coding.  But I imagine this will be different for each coding system)


Thanks for any help,
Tal




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On Sat, Mar 13, 2010 at 8:06 PM, Jean lobry <lobry at biomserv.univ-lyon1.fr>wrote:

> At 23:03 +0200 11/03/10, Tal Galili wrote:
> Hello dear list.
>
> I wish (for my thesis work), to import tRNA data into R and have it
> aligned.
>
> My questions are:
> 1) What resources can I use for the data.
> 2) What commands might help me with the import/alignment.
>
>
> So far, I found two nice repositories that holds such data:
>
> 1) <<http://trnadb.bioinf.uni-leipzig.de/Result>
> http://trnadb.bioinf.uni-leipzig.de/Result><
> http://trnadb.bioinf.uni-leipzig.de/Result>
> http://trnadb.bioinf.uni-leipzig.de/Result
> 2) <<http://gtrnadb.ucsc.edu/download.html>
> http://gtrnadb.ucsc.edu/download.html><
> http://gtrnadb.ucsc.edu/download.html>
> http://gtrnadb.ucsc.edu/download.html
>
>
> And also the  readFASTA command from Biostrings, that does basic importing
> of the data into R.
>
> My problem still remains with how to handle the alignment of the tRNA.
>
> 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).
> If you might be willing to advice me, that would be most helpful.
>
> Many thanks in advance,
> Tal
>
> Hi Tal,
>
> let's start from http://trnadb.bioinf.uni-leipzig.de/Search which is
> a nice ressource and suppose that you are interested in Ala tRNA.
>
> Select the Alanine checkbox and then click on the "search database"
> button. Wait for the search result page. At the bottom, select
> the "select all sequences of search" checkbox, on the scrolling
> menu just on the right select the "send alignment (multiFASTA)"
> and then click on the "submit" button. A file called "fasta.mfa"
> should be downloaded on your computer.
>
> Then under R:
>
> ###
> library(seqinr)
> res <- read.alignment(file.choose(), format = "fasta")
> names(res)
> [1] "nb"  "nam" "seq" "com"
> res$nb
> [1] 605
> ###
>
> The alignment of 605 tRNA sequences has been imported in the
> object called "res", now you can play with it. For instance
> the consensus with the majority rule is:
>
> ###
> consensus(res)
>  [1] "-" "g" "g" "g" "g" "c" "t" "g" "t" "a" "g" "c" "t" "c"
> [15] "a" "g" "c" "t" "-" "g" "g" "t" "-" "-" "a" "g" "a" "g"
> [29] "c" "g" "c" "c" "t" "g" "c" "t" "t" "t" "g" "c" "a" "t"
> [43] "g" "c" "a" "g" "g" "a" "g" "-" "g" "t" "c" "a" "g" "g"
> [57] "g" "g" "t" "t" "c" "g" "a" "t" "c" "c" "c" "c" "c" "t"
> [71] "c" "a" "g" "c" "t" "c" "c" "a" "-" "-" "-"
> ###
>
> HTH,
>
> Z.
>
>
> --
> Pr. Jean R. Lobry (Dr. phil. hab.)
> Head of Laboratoire de Police Scientifique de Lyon
> Institut National de Police Scientifique
> 31 av. F. Roosevelt, F-69134 ECULLY CEDEX
> Allo: +33 (0)4 72 86 89 60
> e-mail: jean.lobry at interieur.gouv.fr
>
>
>
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