ABSTRACT
Summary Here I describe seedVicious, a versatile microRNA target site prediction software that can be easily fitted into annotation pipelines and run over custom datasets. SeedVicious finds microRNA canonical sites plus other, less efficient, target sites. The program also detects near-target sites, which have one nucleotide different from a canonical site. Near-target sites are important to study population variation in microRNA regulation. Among other features, it can also predict targets on alignments and compute evolutionary gains/losses of target sites using maximum parsimony.
Availability and implementation The program is written in Perl and runs on 64-bit Unix computers. Users can also try the program in a dedicated web-server by uploading custom data, or browsing pre-computed predictions. SeedVicious and its associated web-server and database (SeedBank) are distributed under the GPL/GNU license, and available at http://seedvicious.essex.ac.uk/
Contact amarco.bio{at}gmail.com