How to annotate a sequence with its genomic coordinates ?

Question

[Pei]

Hi All:

Do you know how to annotate a sequence, (RNA) by its corresponding genomic coordinates?

That is, how to identify the genomic corrdinates for a RNA sequence?

R-based method would be mostly welcomed.

Thanks in advance!

Best

Answer 1

[Pascal]

If you have nothing but the sequence of your transcript, you probably want to use BLAT to get the genomic coordinates. For a lot of sequences and an automated annotation you can set up your own BLAT server.

Answer 2

[rutial]

What you can also do, is use the auto-annotation feature within Genome Compiler, which is a free software. You can import your file or directly look for it within the software (connected directly to NCBI so you can very easily import the sequence you want). When you open up an un-annotated sequence the software will prompt a message asking if you would like it to auto annotate it. You can also read more about the automatic sequence annotation feature here.