mature-miR coordinates

[Jan]

Hello all there,

For a program I write I need the coordinates of the mature-miR or the
star-sequences, 3p/5p. Right now I use the mirna_mature.txt from
miRBase v.13 but this is a mess and it misses some entries which I
find in your database same version. So I really would like to use
MirMaid but how can I get the coordinates of the matures etc.? I can
access the locus information of the precursor but unfortunately this
feature doesn't exist for the matures, does it?

Thank you very much for your help!
Jan

[Anders Jacobsen]

Hi Jan,

miRMaid does currently not store coordinates for the mature miRNA in order to keep the data model as simple as possible. The technical arguments are that the coordinate information is redundant if you know the sequence of the precursor and the mature, and that there is a many-many relationship between matures and precursors, which would involve an extra association/table to store coordinate information. However, if there is a demand for this kind of information, we could look into making this information available in future releases.

To get relative coordinates for a mature miRNA in a precursor, I suggest that you some programming language to search for the mature substring in the precursor and extract the position for the match. If you want genomic coordinates for the mature, you would need to map these precursor relative coordinates to the genomic coordinates using the locus coordinate information. 

In principle, you could do all these things by with the following three calls to the web service interface (here using miR-107 as an example):

http://current.mirmaid.org/matures/hsa-miR-107.xml # get mature sequence

http://current.mirmaid.org/precursors/hsa-mir-107.xml # get precursor sequence

http://current.mirmaid.org/precursors/hsa-mir-107/genome_positions.xml # get genomic coordinates

I hope this helps.

Cheers,

Anders Jacobsen

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