Translate from hsa-let- to MIMAT type

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6.9 years ago

landscape95 ▴ 190

I am looking for a way to translate from mature sequence name hsa-let- to its Accession number MIMAT type in R, I find the biomaRt but it seems to be not ok. I want to have something like this http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062 From hsa-let-7a-1 to MIMAT0000062 Thanks in advance!

My data: enter image description here

The result from my code:

tmp = getBM(attributes = c("mirbase_id", "mirbase_accession"),
                     values = values,
                     mart = ensembl)

enter image description here

conversion • 2.1k views

ADD COMMENT • link updated 11 months ago by Ram 43k • written 6.9 years ago by landscape95 ▴ 190

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From your data, hsa-let-7a-5p is miRNA' s ID, and it has serval stem-loop hsa-let-7a-1 hsa-let-7a-2 hsa-let-7a-3. So you need translate you data to stem-loop then map to MIMAT type.

ADD REPLY • link updated 11 months ago by Ram 43k • written 6.9 years ago by zjhzwang ▴ 180

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Can you instruct me how to do that?

ADD REPLY • link 6.9 years ago by landscape95 ▴ 190

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You can find what you want from miRbaseDownload site

ADD REPLY • link 6.9 years ago by zjhzwang ▴ 180

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