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Bug fixes to release 20 MySQL database dumps

Read no further unless you care about the MySQL database dumps in the database_files directory on the FTP site.

A couple of people (many thanks Jeff and Jakob) found errors in the the release 20 MySQL database dumps: a small number of new mature sequences were not linked to their hairpin precursors, and the ends of a smaller number of old mature sequences were off by 1. The table affected was mirna_pre_mature. If you’re using these dumps you will probably want to grab the fixed version from the FTP site (timestamp 17/7/2013). You might notice other files in that directory with the same new timestamp — feel free to grab those too, but you are much less likely to care about those (the changes are either cosmetic or updated links to other resources). The FASTA format sequence files, the EMBL format data file, and all other data dumps were unaffected by these bugs.

Apologies for any inconvenience.

Posted in bugs, data update, releases.


6 Responses

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  1. Mickael says

    Hi,
    I’m using the gff coordinates of miRNAs from miRbase and I noticed few problems in hsa.gff (haven’t checked for others). Some pre-miRNAs are listed, but not their miRNAs in 3p and 5p. Here are the faulty entries:
    chr8,hsa-mir-486-2
    chr8,hsa-mir-7112-2
    chr14,hsa-mir-7641-2
    chr14,hsa-mir-8071-2
    chr15,hsa-mir-7973-2
    chr15,hsa-mir-6859-2
    chr16,hsa-mir-6859-3
    chr16,hsa-mir-6511b-2
    chr16,hsa-mir-6770-2
    chr16,hsa-mir-6770-3
    chr16,hsa-mir-6862-2
    I checked few on miRbase website and all had a 3p and 5p miRNAs, so it’s a problem with the gff file.

    Is it easy to correct from your side ? Before I do modifications by hand.

    Thank you for your help

    • sam says

      Yep, you’re right. Apologies for that. I’ve hopefully fixed the problem and new gff3 files are on the FTP site. Thanks!

  2. Ke-xiao Zheng says

    Big thanks for bringing rel. 20 online, a great job!

    Also, i noticed a tiny “issue” in the “mature.fa” file: the “-” symbol between “miR” and number are missing in some miRNA names. For example, all the Arabidopsis thaliana miRNAs are named like “miR156a” instead of “miR-156a”.

    • sam says

      Actually, that’s not a bug. Plant miRNA names are all missing the ‘-’ between ‘miR’ and the number. That’s been the case since miRBase’s start. I believe the plant community uses dash-number to refer to allelic variants, so we want to avoid confusion with that system.

  3. ChiaraGiaco says

    I don’t know exactly if this is the place where to leave this comment, but I found a mistake in the file of human genomic coordinates.
    For miR-450a-1-3p it is indicated that Derives_from=MI0003187 but I think it should be Derives_from=MI0001652 since it is derived from genomic locus 1.

    Best

  4. kaipeng xie says

    UCSC hsa-mir-1302-11 chr19:71973-72110 +
    miRBase 20.0 hsa-mir-1302-11 chr9: 30144-30281 [+]
    They are not on the same chromosome. Is it right ?



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