title: miRNEST database: an integrative approach in microRNA search and annotation.
abstract: Despite accumulating data on animal and plant microRNAs and their functions, existing public miRNA resources usually collect miRNAs from a very limited number of species. A lot of microRNAs, including those from model organisms, remain undiscovered. As a result there is a continuous need to search for new microRNAs. We present miRNEST (http://mirnest.amu.edu.pl), a comprehensive database of animal, plant and virus microRNAs. The core part of the database is built from our miRNA predictions conducted on Expressed Sequence Tags of 225 animal and 202 plant species. The miRNA search was performed based on sequence similarity and as many as 10,004 miRNA candidates in 221 animal and 199 plant species were discovered. Out of them only 299 have already been deposited in miRBase. Additionally, miRNEST has been integrated with external miRNA data from literature and 13 databases, which includes miRNA sequences, small RNA sequencing data, expression, polymorphisms and targets data as well as links to external miRNA resources, whenever applicable. All this makes miRNEST a considerable miRNA resource in a sense of number of species (544) that integrates a scattered miRNA data into a uniform format with a user-friendly web interface.
authors.affiliation: Laboratory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland. miszcz@amu.edu.pl
authors.forename: Michał Wojciech
authors.initials: MW
authors.lastname: Szcześniak
authors.forename: Sebastian
authors.initials: S
authors.lastname: Deorowicz
authors.forename: Jakub
authors.initials: J
authors.lastname: Gapski
authors.forename: Łukasz
authors.initials: Ł
authors.lastname: Kaczyński
authors.forename: Izabela
authors.initials: I
authors.lastname: Makalowska
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D012367:RNA, Viral