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

[Jean lobry]

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