Help for a newbie in here please!

[andresroca]

Hello everyone and thanks for your help. Im a medical doctor doing a masters in molecular biology and i have bioinformatics as one of my classes. My problem is that i have no idea about this and i have to come up with a scrip using shell to download the non coding ribosomal RNAs of all genomes in the ensemble.org site in FASTA format. I would really apreciate your help, thanks a lot!

[simonandrews]

You have two choices really.

You could use the official Ensembl Perl API to write a script to specifically pull out only the genes you want from the database directly. This is probably the 'neatest' solution, but the Ensembl API is not something you're going to get on top of in a short time. It's very powerful but it's also complex, opaque and the documentation is scattered all over the place. It might be an interesting learning experience, but probably not the quickest way to get the job done.

The other alternative is that you could pull the full list of ncRNAs from the Ensembl FTP site. The site has a consistent structure so it should be possible to iterate through the various species directories to pull out the ncrna file for each one within a script. Having done that you'd need to go through the files you downloaded to extract only the ribosomal RNAs from the full set, which you might have to do with a simple set of naming rules.

[jiaco]

wget -r -nd -A *.ncrna.fa.gz ftp://ftp.ensembl.org/pub/release-69/fasta

this seems to work.

[andresroca]

Wowww, thanks a lot guys, safe to say that you saved my semester and my sanity! glad to know kind people!