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...
3 answers
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.
Try Galaxy
- Upload your co-ordinates into ucsc using #GetData-"UCSC Main"
- Select your desired genome assembly and paste the co-ordinates using "region" - "position" options.
- Click "get output"
- You can see "Create one BED record per:" option. This allows to extarct UTR, exotic and intronic sequences of your input.
I think you should be more specific than that - perhaps indicating the workflow and tools that would solve the problem
UCSC table browser (selecting Known genes table) lets you define detailed regions to check for the presence of exons introns and cds
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