Getting Sequence Data From Ensembl With Variations

Question

[calvinchong]

I have been trying to get sequence with ensembl with variation in order to produce sequences suitable for input to PrimerBlast (NCBI) as input, to provide primers suitable for Sanger sequencing. However, I have tried but cannot figure out the way to do it on perl. Currently, I am using ensembl biomart to export sequences with exon boundaries and parse it with perl.

Any better methods, preferably totally in a perl script? Thanks.

Answer 1

[Emily]

Ensembl have a Perl API. There's an online course on using it here: http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop

[calvinchong]

Thanks. Though the site is currently down, I'll bookmark it and have a look. In fact, I have looked at the API tutorials on the ensembl website (the text not the recorded video) but it seems that what I wanted to do is between the level of the tutorials and the API specification which is quite arcane to me...

Do you know places where I can find examples and learn from them?

[Emily]

The new online course has loads of example scripts that you can take and cannibalise as you will.

[calvinchong]

Thanks. Will read.