title: AnnotateGenomicRegions: a web application.
abstract: BACKGROUND
  Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software.
  
  
  RESULTS
  Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user.
  
  
  CONCLUSIONS
  The increasing spread of genomic technologies generates the need for a simple-to-use annotation tool for genomic regions that can be used by biologists and bioinformaticians alike. AnnotateGenomicRegions meets this demand. AnnotateGenomicRegions is an open-source web application that can be installed on any personal computer or institute server. AnnotateGenomicRegions is available at: http://cru.genomics.iit.it/AnnotateGenomicRegions.
authors.forename: Luca
authors.initials: L
authors.lastname: Zammataro
authors.forename: Rita
authors.initials: R
authors.lastname: DeMolfetta
authors.forename: Gabriele
authors.initials: G
authors.lastname: Bucci
authors.forename: Arnaud
authors.initials: A
authors.lastname: Ceol
authors.forename: Heiko
authors.initials: H
authors.lastname: Muller
mesh_terms: D000818:Animals; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D051379:Mice; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software; D015027:Zebrafish / Q000235:genetics