UCbase 2.0: ultraconserved sequences database (2014 update)

Vincenzo Lomonaco; Riccardo Martoglia; Federica Mandreoli; Laura Anderlucci; Warren Emmett; Silvio Bicciato; Cristian Taccioli

doi:10.1093/database/bau062

UCbase 2.0: ultraconserved sequences database (2014 update)

Database (Oxford). 2014 Jun 19:2014:bau062. doi: 10.1093/database/bau062. Print 2014.

Authors

Vincenzo Lomonaco¹, Riccardo Martoglia¹, Federica Mandreoli¹, Laura Anderlucci¹, Warren Emmett¹, Silvio Bicciato¹, Cristian Taccioli²

Affiliations

¹ Computer Engineering Department, University of Modena, Via Campi 213/b, 44100, Modena, Department of Statistical Sciences, University of Bologna, Via Belle Arti 41, 40126, Bologna, Italy, Department of Genetics, Environment and Evolution, Genetics Institute, University College London, London, WC1E 6BT, UK and Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Via G. Campi 287, 41100, Modena, Italy.
² Computer Engineering Department, University of Modena, Via Campi 213/b, 44100, Modena, Department of Statistical Sciences, University of Bologna, Via Belle Arti 41, 40126, Bologna, Italy, Department of Genetics, Environment and Evolution, Genetics Institute, University College London, London, WC1E 6BT, UK and Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Via G. Campi 287, 41100, Modena, Italy cristian.taccioli@unimore.it taccioli@gmail.com.

Abstract

UCbase 2.0 (http://ucbase.unimore.it) is an update, extension and evolution of UCbase, a Web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase 2.0 is a platform-independent Web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for Single Nucleotide Polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase 2.0 now includes a graph visualization interface directly linked to UCSC genome browser. Database URL: http://ucbase.unimore.it.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Conserved Sequence*
Databases, Genetic*
Humans
Mice
Polymorphism, Single Nucleotide / genetics
Rats
Search Engine
Software*
User-Computer Interface