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

Highlights

  • Ultraconserved sequences (UCRs) are genomic sequences that were found identical comparing human, rat and mouse genomes [1]

  • UCbase 2.0 is a platformindependent Web resource that includes the updated version of the human genome annotation, 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

  • Several other resources are currently available for the analysis of ultraconserved sequences (UCRs), e.g. UCNEbase [19], cneViewer [20], CONDOR [21], VISTA Enhancer browser [22], Ancora [23], ECR browser [24], TFCONES [25], FANTOM 5 enhancer atlas [26] and FANTOM 5 promoter atlas [27]

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Summary

Introduction

Ultraconserved sequences (UCRs) are genomic sequences that were found identical comparing human, rat and mouse genomes [1]. Major improvements of the Web user interface are aimed at facilitating the extraction of relevant information about genes in which the UCRs are located In this updated version it is possible to investigate if genes containing UCRs have SNPs or undergo splicing events. UCRs located in that specific genomic region, whereas ‘query type 5’ outputs a table containing all pathologies related to the gene or chromosome region in which a particular UCR is located (Figure 5). The new BLAST-based search query instead allows matching a sequence against the entire UCR sequence database (‘query type 6’) and optionally provides the new opportunity to filter results for the UCRs located in genes involved in specific pathologies (Figure 6). To retrieve all the GENE_BIOTYPE features (miRNA, lincRNA, antisense, etc.) from the GENE table, the query is: SELECT DISTINCT GENE_BIOTYPE FROM GENE

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