A comprehensive review and uniform system for annotation of miRNA genes and families can be found here

Article A Uniform System for the Annotation of Vertebrate microRNA G...

Maybe you can match them there-> http://xfam.org/

(from https://www.biostars.org/p/1838/)

or even here:

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mirpath/index

At best you look at the homepage of companies selling LNA antagomirs and make an enquiry to their support team if they have an offer or how to proceed.

I am not familiar with miRNAs in animals, but I got interested in this question. Is family well defined for miRNAs in animals? In plant it is not. Therefore answering your question is not easy. We need a definition to have a grouping criterion. One possibility would be to cluster the sequences at some identity threshold, eventually focusing only on the seed sequence.

I looked at the publication. Would it be ok for you to have a tool that gives you a minimal set of 8mers (the length of the tiny LNAs) covering all your miRNAs?

miRNA families can be found here for human (and a few other species):

http://www.targetscan.org/cgi-bin/targetscan/vert_70/mirna_families.cgi?db=vert_70&species=Human

You can also look at sequence alignment with Jalview for example:

http://www.jalview.org/

and focus on seed sequences (nucleotides 2 to 7 or 8 from 5' end). In agreement with Oscar statement. Then, it's better to separate into clusters as I expect a few (not just one) seed sequence to be enriched.

Due to the mechanism of binding, animal (strong importance of the seed) and plant (the whole sequence should show near perfect match with the target) miRNAs behave very differently.

Last but not least, in our lab we got easier to interpret results with overexpression of the microRNAs (mimic) than repression (LNA). You could also test your 80 miRNAs in parallel using multi-channel pipettes and multi-well plates.

http://www.targetscan.org/cgi-bin/targetscan/vert_70/mirna_families.cgi?db=vert_70&species=Human

http://www.jalview.org/

A comprehensive review and uniform system for annotation of miRNA genes and families can be found here

Article A Uniform System for the Annotation of Vertebrate microRNA G...

The members of a same miRNA may differ in the seed region  and even one basepair difference between them can change their interaction with the target. For example, we found miR-27a to regulate a our gene of interest but not miR-27b. I think you should first narrow down your list of miRNAs by using TargetScan algorithm where in you can choose miRNAs with more number of binding sites on your target mRNA and also those who are broadly conserved among many species.  After this, you could overexpress  these miRNAs inside cells to observe the effect on endogenous levels of your target protein and then go for antimiR experiments.

Many thanks for your great answers. I need some time to go through all the proposed options here, so when I'm done I will be happy to return my results and share them for further discussion if somebody is still interested.

A the moment I'm going through my list manually maching it with my target sequence, similiar to what Raihana has proposed.

Dier Soner-Öber Sienen!

You can also try tha above mentioned site:

http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000462

Sincerely,

Otilia

Dear Otilia,

thank you for the link, I already use mirbase on a daily basis but for my purposes it wasn't useful.

But, I found a web tool which was quite helpful, so I would like to share this information in case somebody faces similiar tasks. There, you can align a list of miRNAs against a single or multiple target gene(s) an it gives you a prediction of whether your gene of interest might be regulated by the miRNAs. Several other options are also available.

http://mirtar.mbc.nctu.edu.tw/human/

There also databases for mouse, rat and dog so I think a lot of people could actually profit from it. So far, I didn't experienced any downsite and the alignments kind of made sense, allthough I'm not sure which algorithm is beeing used. If anybody have some additional information about this product please share.

Align them and look at the seed sequence... if they match, they should be classified as one family.

Dear Muriel,

thanks for the advice. I already did an aligment with ClustalW but it didn't come out like I'd expected. However I extracted the canonical seed sequence binding sites manually and was able to identify some families. Unfortunately there were very little similarities so now I went and selected miRNAs with the highest binding probabilities (8mer, 7mer-m8, 7mer-A1). That left me with a bunch of miRNA which I'll hopefully be able to test.

Hi Folks,

I discovered another useful tool that predicts the repression strength of miRNAs on a given target. You can use both custome and database based sequences to perform the prediction. I found it to be very helpful.

http://mirmap.ezlab.org/app/