1
$\begingroup$

Does anyone know of tools to convert lists of miR names to their miRBase Accession IDs? I know they exist, but my search keeps pulling up gene ID converters.

EDIT: both @rg255 and @shigeta have provided solutions to the underlying issue, but I am curious to know if something exists for miRNAs that is similar to a site like this.

EDIT 2: miRNA names are of the form 'hsa-let-7a' and Accession IDs are of the form 'MI0000060'

$\endgroup$
2
  • 2
    $\begingroup$ in what species? this website looks like it will have them mirbase.org/cgi-bin/browse.pl?org=hsa If you are trying to connect them to data I'd suggest you find the table you want, save it in to a .txt file and use R to match them up. $\endgroup$
    – rg255
    Mar 12, 2013 at 8:17
  • $\begingroup$ Somehow, I completely missed that page. Thanks! (If you wanted to post that as an answer, I'd accept it.) $\endgroup$
    – blep
    Mar 12, 2013 at 15:07

2 Answers 2

1
$\begingroup$

in what species? this website looks like it will have them mirbase.org/cgi-bin/browse.pl?org=hsa If you are trying to connect them to data I'd suggest you find the table you want, save it in to a .txt file and use R (using the merge() function - df=merge(df1,mirbase,by="miR_names") would be a rough guide) to match them up.

Here is a batch converter - http://atlas.dmi.unict.it/mirandola/tools.php - add the text list to box on the right and it produces a table.

$\endgroup$
5
  • $\begingroup$ Thanks, especially, for pointing out the merge function; I hadn't considered a solution in R. (The only issue I see is that this particular table doesn't include mature miRNA IDs, but it's a useful list for other reasons.) $\endgroup$
    – blep
    Mar 12, 2013 at 23:17
  • $\begingroup$ @dd3 see added batch converter tool - but could you post an examples of what "miR name" and "miRBase Accesion ID" typically look like so I can tell when I find the right thing. I.e. are you expecting a sequence of numbers, letters, alphanumeric sequence, symbols, a word, a sentence, or (albeit unlikely) an extract from a Shakespeare text... thanks $\endgroup$
    – rg255
    Mar 13, 2013 at 7:40
  • $\begingroup$ This is what I meant. I know this wasn't part of my question, but do you have any idea whether something like this exists for mice? $\endgroup$
    – blep
    Mar 13, 2013 at 7:48
  • $\begingroup$ no idea I'm afraid $\endgroup$
    – rg255
    Mar 13, 2013 at 7:54
  • $\begingroup$ Well, thanks for all of your work on this question, especially with the repeated edits. (I'll work on making future questions clearer from the start.) $\endgroup$
    – blep
    Mar 13, 2013 at 8:00
1
$\begingroup$

If you want it all, download the mirRNA.xls.zip file from mirbase here:

ftp://mirbase.org/pub/mirbase/CURRENT/

its a spreadsheet that includes these data as columns and also more information besides - for the entire database.

$\endgroup$
2
  • $\begingroup$ bulk downloads in columnar format are always the way to go :) $\endgroup$
    – shigeta
    Mar 12, 2013 at 20:51
  • 1
    $\begingroup$ That, and Python. I think I make dictionaries for everything. $\endgroup$
    – blep
    Mar 12, 2013 at 21:22

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .