How (and where) to get aligned tRNA sequences (and import it into R)

Posted by Tal Galili on Stack Overflow See other posts from Stack Overflow or by Tal Galili
Published on 2010-03-11T21:03:16Z Indexed on 2010/03/11 21:09 UTC
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(This is a database / R commands question)

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:

http://trnadb.bioinf.uni-leipzig.de/Resulthttp://trnadb.bioinf.uni-leipzig.de/Result
http://gtrnadb.ucsc.edu/download.htmlhttp://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

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