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The Zebrafish new assembly (Zv9) has been out (in Ensembl and UCSC) for a while, yet the miRNA tracks in miRBase has not been updated yet. Does anyone has an idea, when the miRNA annotations in Zv9 be released.
I don’t think miRBase has had a release since Zv9 came out. Each time we build a release we aim to use the most recent assemblies in EnsEMBL and elsewhere, so next time will include coordinates on the Zv9 release. In the meantime, the gff file of coordinates on Zv8 (ftp://mirbase.org/pub/mirbase/16/genomes/dre.gff) can be lifted over to Zv9 at UCSC (http://genome.ucsc.edu/cgi-bin/hgLiftOver).
Hi, could you please check the mmu-mir-378 entry? The website says for the precursor hairpin:
but your bulk download file hairpin.fa (release 18) sequence is shorter:
>mmu-mir-378 MI0000795 Mus musculus miR-378 stem-loop
which gives problems when aligning to this file because you cannot find mature
And are there perhaps more such cases? Thanks.
PS: mmu-miR-151 is another such case where the hairpin.fa sequence is truncated and so excludes mature mmu-miR-151-3p…
The sequences are all complete in the hairpin.fa file. The shorter sequence you show is just the first line of the hairpin sequence. All entries longer than 60nts span more than one line in that file.
I am new to the world of microRNA, and I am trying to figure out all of the rules of nomenclature and understanding the information in the database. Can someone explain what exactly “reads per million” or RPM means? I know it relates to expression of the microRNA, but what exactly is a “read” and how is this calculated?
Nevermind; I found the tutorial https://www.softchalkcloud.com/lesson/files/Ii14UlfmgGAoZy/index.html
I just wandered why there are no miRNAs from protozoan parasites deposited in the miRBase. For example, there are papers by Wang C team on Giardia lamblia miRNAs that are validated by Northern blot and other techniques (for example: Li et al, 2012. Cellular Microbiology 14, 1455-1473). Also from Toxoplasma gondii (Braun L et al 2010 Plos Pathogens Volume 6, Issue 5 e1000920. Did you ever received these miRNAs?
We do have a few non-animal, non-plant miRNAs that have been published and submitted to us. The sets we don’t have were not submitted, or it was agreed with authors not to deposit them. There is some controversy in the community about these. This paper for example implies that these sequences are not likely to be miRNAs:
Tarver JE, Donoghue PC, Peterson KJ. Do miRNAs have a deep evolutionary
history? Bioessays. 2012 34(10):857-866. doi: 10.1002/bies.201200055
As I understand it, many protozoans (most trypanosomes for example) don’t have the RNAi machinery, so won’t have miRNAs by the current definition. That does not of course mean that they don’t have interesting small RNAs.
A new paper just came up in Journal of Integrative Bioinformatics:
“Can MiRBase Provide Positive Data for Machine Learning for the Detection of MiRNA Hairpins?” by Saçar et al. 2013.
Maybe some points could be answered from miRbase staff.
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