Hi, I need to get a list of miRNAs that located on certain chromosomal bands. If there is any bioinformatic tool or website where I can find this information, please share.
Thanks
Hi, if organism of your interest is in Ensembl database you can do it easily via BioMart. You should select organism (Dataset option), region (chromosome and band by start/end) at Filters->Region option, and type of gene at Filters-> GENE option (for example Limit to genes “with miRBase IDs” in drop-out menu).
Then you should select gene attributes to save (location, IDs etc). Then proceed with Result button at the upper left corner of the window.
Hope this information will help.
You may also try the search function of miRBase via http://www.mirbase.org/search.shtml.
At the search page, you just specifi the 'species', 'chromosome', 'start pos.' and 'end pos.', then miRBase report the miRNAs within your specified genomic region.
How can I use BioMart in EnsemblPlants to get a chromosome picture showing/ locating only my genes of interest or to get a synteny?
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