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.
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Chuangye •
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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Paulo Nuin
Do you think I should make databases for each miRNA family and blast the novel miRNAs sequences to each miR family databases?
What do you have? You have pure miRNA sequences, large segments? Are all of them novel or already known?
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.
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.
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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Lars Juhl Jensen
Thank you. I think it is a good way to determine novel miRNAs.
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.
No and for good reasons: the current version of Rfam is from January and miRBase 15 was released in April ;)
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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