Mirna Predictions In Plants

Question

[vandanabioinfo23]

I have a question regarding miRNA prediction (known) in plants. I want to know that what standalone version tool I can use for miRNA prediction- bioinformatics analysis

Answer 1

[Mike Axtell]

If you are looking for miRNA annotations based on homology to known miRNAs from other plants, you could try microHARVESTER, although I don't know if their web server it still running, it was down just now when I checked.

If you are looking for miRNA annotations from reference-aligned small RNA-seq data, there are lots of choices, including ShortStack, miRDeep-P, miRDeepFinder , and miRCAT

Answer 2

[JC]

There are several tools, I have used before MiRanda http://www.microrna.org/microrna/getDownloads.do and psRNATarget http://plantgrn.noble.org/psRNATarget/

This site contains more programs -> http://mirnablog.com/microrna-target-prediction-tools/

[Mike Axtell]

Note these are miRNA-target prediction programs, not miRNA locus prediction programs which (I think?) vandanabioinfo23 was looking for.

Answer 3

[Mary]

I was just noticing in the new banana genome paper (the one with the Venn diagram everyone is talking about) had a link to a plant microRNA database and it has some prediction functions. http://bioinformatics.cau.edu.cn/PMRD/