microRNA in miRBase and hg19 annotion

[bioworker]

I found there are 1771 microRNA annotated in hg19 annotation data, but in miRBase, there are only about 1100 microRNA. Does anyone know whey they are different and how their ID mapped(they use different gene ID)?
Thank you very much.

[Bert]

I can only speak for Ensembl, but we have for human 1809 miRNAs. Our annotation procedure is as follows: "miRNAs are predicted by BLASTN of genomic sequence slices against miRBase sequences. All species are used. The BLAST hits are clustered and filtered by E value and the aligned genomic sequence is then checked for possible secondary structure using RNAFold. If evidence is found that the genomic sequence could form a stable hairpin structure, the locus is used to create a miRNA gene model. The resulting BLAST hit is used as supporting evidence for the miRNA gene. Note: The miRNA identifier and name are only associated to the resulting Ensembl miRNA if they are of the same species." In other words, some of the miRNA genes in Ensembl are based on evidence from other species than human. How UCSC annotates miRNAs I don't know.

[bioworker]

Hi Bert, thank you very much. I got it.

[metin.ceyhan]

miRNA sequence blast

who can say me, how can we blast a sequence with miRNA, ı ask this ı have a sequence that ı think miRNA so ı want to match other miRNAs but ı dont found blast web site for miRNA sequence

[NicoBxl]

you can create your own blast db with formatdb -i mirbase.fasta -p F
or check the mirbase website : http://www.mirbase.org/search.shtml (but it's not very practical if you've a lot of sequence to blast )