Retrieving Features From Certain Position On Genome

Question

[vaushev]

I would be grateful if anyone can point me to the most appropriate way of querying some genome database (NCBI's, UCSC's - whatever) in order to get features located on my position of interest. By features, I mean I want to know if it is exon, intron, UTR or something else. By far, I tried to query the UCSC's DAS with something like this: http://genome.ucsc.edu/cgi-bin/das/hg19/features?segment=10:7866279,7866281;type=refGene - this gives me some info but not exactly the features that I need...

Thanks in advance!

UPD. thanks all for the suggestions; unfortunately I am not allowed to add more comments yet - I have to wait for 6 hours since registration - what a crazy rules...

[Neilfws]

Those rules are in place to prevent spam bots and they work very well.

[Istvan Albert]

apologies for precluding you from commenting, as Neilfws said it is a spam protection but I will make a change to not count the comments as those (so far) have been less spammy

Answer 1

[brentp]

you can do this with cruzdb in python:

from cruzdb import Genome
[x.features(7866279, 7866281) for x in Genome('hg19').bin_query('refGene', 'chr10', 7866279, 7866281)]

will print:

[['intron', 'cds']]

meaning that it covers an intron and a CDS. If you pull up this region in the genome browser you can see that it spans an intron-exon junction.

Answer 2

[biorepine]

Try Galaxy

1. Upload your co-ordinates into ucsc using #GetData-"UCSC Main"
2. Select your desired genome assembly and paste the co-ordinates using "region" - "position" options.
3. Click "get output"
4. You can see "Create one BED record per:" option. This allows to extarct UTR, exotic and intronic sequences of your input.

[Istvan Albert]

I think you should be more specific than that - perhaps indicating the workflow and tools that would solve the problem

[vaushev]

well, they seem to have huge amount of tools - could you give a bit more details? Thanks!

[biorepine]

It is easier to read galaxy basic tutorial than writing up all the steps. I would suggest you to go through the basic galaxy tutorial. Anyway I updated my answer.

Answer 3

[ff.cc.cc]

UCSC table browser (selecting Known genes table) lets you define detailed regions to check for the presence of exons introns and cds