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Article

Title: A Guide through Present Computational Approaches for the...

Author: Sethupathy, Praveen; Megraw, Molly; Hatzigeorgiou, Artemis G Article Type: Product Analysis
Source: nature methods, v3 n11 p881(6) Publication Date: Nov 2006
  ISSN: 1548-7091
  Illustrations: Tables, Charts, Graphs
URL of Publication: http://www.nature.com/naturemethods

A guide through five widely used mammalian target prediction programs for computational microRNA (miRNA) is provided. In 2001, many additional miRNAs were discovered experimentally and found to be abundant and widespread. In 2003, some groups independently developed the first computational miRNA target predication that concentrated on the fruit fly and mammalian genomes. miRNA target sites can be classified in three categories: (i) 5-dominant canonical, (ii) 5-dominant seed only, and (iii) 3-compensatory. The basic features of the computational target prediction programs analyzed are listed in a table. They perform two steps: identification of potential miRNA binding sites according to specific base-pairing rules and implementation of cross-species conservation requirements. Topics covered are the benchmark set, current target prediction programs (with Web sites and organisms), features used by the mammalian target prediction programs (that were considered in a comparative study in which identifier conversion tables from the Ensemble Web site were used to map all identification types to one standard type), false positive rate, comparison of individual programs, program combinations, sensitivity and number of total predictions for each program, and a practical guide for prediction of miRNA targets.

Special Features: Tables, Charts, Graphs

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miRNA (MicroRNA)

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