Question: Mirna Predictions In Plants
0
gravatar for vandanabioinfo23
8.2 years ago by
Punjab-Mohali
vandanabioinfo230 wrote:

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

plant prediction mirna • 5.5k views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 8.2 years ago by vandanabioinfo230
2
gravatar for Mike Axtell
7.1 years ago by
Mike Axtell240
Penn State University
Mike Axtell240 wrote:

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

ADD COMMENTlink written 7.1 years ago by Mike Axtell240
0
gravatar for JC
8.2 years ago by
JC11k
Mexico
JC11k wrote:

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/

ADD COMMENTlink written 8.2 years ago by JC11k

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

ADD REPLYlink written 7.1 years ago by Mike Axtell240
0
gravatar for Mary
8.2 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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/

ADD COMMENTlink written 8.2 years ago by Mary11k
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