Mirna Sequence Using Biomart R Package

Question

[ayamitjyoti12]

Hi,

How to download the miRNA sequences using BiomaRt package in R.

Thanks

[Neilfws]

Please provide more details. Biomart requires some filters as input - normally IDs of some kind. What do yours look like? Which organism?

[ayamitjyoti12]

Thanks for your reply

I want to download the mature miRNA sequences of human beings and my accession id's look like MIMAT0000001,MIMAT0000219... I am not sure , these may be mirbase id's.

[Emily]

Those are mouse miRBase accessions. Are you looking to get the sequences of human orthologues?

Answer 1

[Assa Yeroslaviz]

your IDs are miRBase Accession IDs of mature miRNAs.

I don't think there is a way to download the sequences from biomaRt. But why don't you use the miRBase ftp server?

There you can download the mature.fa file, which contains all the sequences of known mature miRNA. Upload this file into R and merge your input list with the sequences in the miRBase list.