R help - Mar 2010 - How (and where) to get aligned tRNA sequences (and import/align it using R)

Hi all,
I already posted this to seqinr-forum@lists.r-forge.r-project.org but since
(so far) no reply was given, I decided to try my luck in this list too.


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
2) <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, what command to use or even where to
ask).
If you might be willing to advice me, that would be most helpful.

Many thanks in advance,
Tal


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