Mirna Family Classification
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13.9 years ago
Chuangye ▴ 80

Hi, if I have identified quite a few miRNAs in one organism, and I want to determine which miRNA family that they belong to. shoud I check it one by one to the existing miRNA families ? Could you tell me how to classify them? Thank you.

mirna classification • 11k views
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13.9 years ago
Paulo Nuin ★ 3.7k

You can try miRBase. Either search their web page or download the miRNA coordinates from here. You can try matching the sequences you might have to their database.

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Do you think I should make databases for each miRNA family and blast the novel miRNAs sequences to each miR family databases?

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What do you have? You have pure miRNA sequences, large segments? Are all of them novel or already known?

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Thank you,Paulo. I have many miRNA sequences of several organisms that determinded by computational method.Now I want to classify them into miR family respectively.

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One idea then is to make a blast db from miRBase and blast your sequences against it, although it might be a little hard to find good hits due to the size, but it's a start. Another idea is to see if there's a service (need to check that) that can search multiple sequences on a miRNA database, maybe not miRBase.

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13.9 years ago

I am not an expert on miRNAs, but my suggestion would be to take a look at Rfam. It has a batch search interface that allows you to upload a multi-fasta file with all your sequences in one go.

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Thank you. I think it is a good way to determine novel miRNAs.

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But it couldn't identify the miR family for new miRs such as hsa-mir-4329,hsa-mir-3119-1 et el in miRBase 15.

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No and for good reasons: the current version of Rfam is from January and miRBase 15 was released in April ;)

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13.2 years ago
Dick • 0

Does anybody know of any database that groups miRNas by their families? Thanks

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hi dick, as mentioned before, miRBase is a comprehensive db that you can access and download, you can then classify the miRs by their name. also, if you want to ask a question, you shouldnt do it by posting an answer. but since your question is very similar to this one im not sure its a whole new question.

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12.8 years ago
Madhan ▴ 250

Hi Dick,

You can see the TAM tool which provide miRNA family information

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