title: miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments.
abstract: We present a new version of miRanalyzer, a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. The new version has been notably improved regarding speed, scope and available features. Alignments are now based on the ultrafast short-read aligner Bowtie (granting also colour space support, allowing mismatches and improving speed) and 31 genomes, including 6 plant genomes, can now be analysed (previous version contained only 7). Differences between plant and animal microRNAs have been taken into account for the prediction models and differential expression of both, known and predicted microRNAs, between two conditions can be calculated. Additionally, consensus sequences of predicted mature and precursor microRNAs can be obtained from multiple samples, which increases the reliability of the predicted microRNAs. Finally, a stand-alone version of the miRanalyzer that is based on a local and easily customized database is also available; this allows the user to have more control on certain parameters as well as to use specific data such as unpublished assemblies or other libraries that are not available in the web server. miRanalyzer is available at http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php.
authors.affiliation: Departmento de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain. mlhack@gmail.com
authors.forename: Michael
authors.initials: M
authors.lastname: Hackenberg
authors.forename: Naiara
authors.initials: N
authors.lastname: Rodríguez-Ezpeleta
authors.forename: Ana M
authors.initials: AM
authors.lastname: Aransay
mesh_terms: D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000032:analysis / Q000737:chemistry* / Q000378:metabolism*; D018749:RNA, Plant / Q000737:chemistry; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant