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

[Jean lobry]

>  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
>  <http://gtrnadb.ucsc.edu/legend.html>legend 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

Hi Tal,

I'm not aware of tools under R to align tRNA sequences, based on
secondary structure or not. The best IMHO is to start from a
database where the job was already done to avoid re-inventing
the wheel. In my previous example we wouldn't have been able
to compute a consensus sequence with the simple majority rule
if the alignment was a mess.

It's always a good idea to check the the quality of an alignment,
you can do this easily under R by inspecting it in a spreadsheet-
like environment this way:

###
resmat <- as.matrix(res)
fix(resmat)
###

Now, depending on your goals and skills you may also consider
implementing your own tRNA alignment utility, but I suspect
this will involve some encoding at C level for efficiency
purposes.


Best,

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