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

Question

(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:

• tRNAdb at the University of Leipzig
• Genomic tRNA database at UCSC

And also the readFASTA command of the Biostrings R Package, 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

Answer 1

The two databases you have listed look like a good place to start. Here's another: tRNADB-CE.

Obtaining a curated dataset can save you a lot of headaches. Have you looked for any good review papers on tRNA genes that might point to "gold standard" tRNA databases currently used in the field?

Another way to go about building a tRNA sequence database would be to use sequences tagged with Geno Ontology (GO) terms related to tRNA function. You can search for GO terms such as "trna" using AmiGO and then retrieve all sequences tagged with the specific GO terms that you care about. I would recommend starting with a curated database, however.

Given that your sequence data is in FASTA format (which it probably will be), three common utilities for multiple sequence alignment are: clustalW, MUSCLE, and T-Coffee.

Since you are working in R, here is an R package that will allow you to make calls to MUSCLE (you will need to install the stand-alone MUSCLE utility as well). Parsing the output from the alignment programs is not difficult, but this package may save you a little effort.

Good luck.