plant microrna database

Web Resources for Plant Scientists

by Christoph on October 16, 2009

miRU: Plant miRNA Potential Target Finder
http://bioinfo3.noble.org/miRNA/miRU.htm

This website allows users to predict plant miRNA target genes.  By entering a small RNA sequence (19-28nt) the program will report all potential complimentary sequences.

PlantGDB
http://www.plantgdb.org/

This website is dedicated entirely to plant miRNA and provides many useful tools such as sequence browser & assemblies, genome browser, and other tools and datasets.

PMRD:  plant miRNA Database
http://bioinformatics.cau.edu.cn/PMRD/

This site offers a complete list of all publicly known plant miRNA sequences.  The database is composed of a total of 8,433 sequences including all known sequences in the miRBase database.

UPC: A Resource for Predicting and Comparing Plant microRNAs
http://www3a.biotec.or.th/micropc/index.html

Here users can predict and compare plant miRNA sequences.  This site includes 128 miRNA families, 125 plant species, and 2,995 protein targets.

The UEA plant sRNA toolkit
http://srna-tools.cmp.uea.ac.uk/targets/

Users can input sequences up to 50 nucleotides in length in FASTA format to run target predictions for their sequence dataset.

Incoming search terms for this article:

{ 2 comments }

Plant microRNA Database Goes Online

by Chris on October 8, 2009

The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated by the database organizers. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser.

In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, the possible target genes for each miRNA with a predicted interaction site are included in the database.  In addition, some miRNA expression profiles are provided in the PMRD.

The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD.

  1. Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z.  (2009) PMRD: plant microRNA database.  Nucleic Acids Res  [Epub ahead of print]

Incoming search terms for this article:

{ 0 comments }