And it is said to do it by doing: "Structural alignments are generated by aligning tRNA sequences against domain-specific tRNA covariance models with the use of COVE."
Which leads me to my questions:
Where might I find the "domain-specific tRNA" to run the COVE model with?
How can I do this on windows?
Is there a better way to do this alignment?
This is my first question, and I am very new to bioinformatics, so I am sorry if I am missing something very basic, or am asking something to which not many people would know to answer.
Maybe, you should be more specific about what you really want to do? It looks a bit like you already have the solution in the web-site you linked. So, what do you really want to do with your tRNA sequences, what is the problem you are trying to solve?
This would really help people to provide a good answer.
Michael - what I really want is to compare (some areas of, for example, the D loop in) tRNA's from different species.
In order to do so, I need to know that I am looking at the D loop in all of them, but it is located in different numbering in different tRNA's from different species. I could just copy paste the websites result (for an aligned sequence, based on the COVE model and the secondary folding of the tRNA) - but I had hoped for a more generic (and thus, scalable) solution for getting these aligned sequences (then using copy paste).
Thanks darked.
I am at home now and can't access the file. I'll try it once I get to the University (I am not sure if they have access or not). Thanks!
The site is a little short on information but it gave me the impression that it will build the covariance model from the multiple sequence alignment itself. Try contacting the author for more information.
You can compile cove on Windows under Cygwin, I just gave it a try and compiled it with no problem.
I had a quick look into the documentation of the software. If you donwload and unpack the soucecode archive, there is a Guide.tex file that can be compiled with Latex, you could look into this. So, to answer your questions partially without trying anything myself:
Where do I find the covariance Models to run COVE with? As Istvan said: you have to make them yourself. From the manual:
Using these programs, you can:
generate new models, by training them on example sequences (covet) ....
See Istvan's answer
Possibly not:
The tRNA identification program tRNAscan-SE is based on a tRNA CM and COVE (Lowe and Eddy, 1997).
And this program is still state-of-the art in tRNA discovery. If you want to look at RNAs in general an learn about their structure then Rfam/Infernal is nice.
If you are interested in RNA structure and visualization the BiBiServ RNA-Studio are an interesting resource.
the program you linked is 14 years old and has the phrase 'old version' in its description. Are you sure you want to use it?
Maybe, you should be more specific about what you really want to do? It looks a bit like you already have the solution in the web-site you linked. So, what do you really want to do with your tRNA sequences, what is the problem you are trying to solve? This would really help people to provide a good answer.
Giovanni - if I where to find a newer better software I would gladly use it :)
Michael - what I really want is to compare (some areas of, for example, the D loop in) tRNA's from different species. In order to do so, I need to know that I am looking at the D loop in all of them, but it is located in different numbering in different tRNA's from different species. I could just copy paste the websites result (for an aligned sequence, based on the COVE model and the secondary folding of the tRNA) - but I had hoped for a more generic (and thus, scalable) solution for getting these aligned sequences (then using copy paste).