UCbase & miRfunc is the first database containing the long 481 ultraconserved sequences discovered in the genomes of human, mouse and rat by Bejerano et al.
) and identified as disregulated in cancer by Calin et al.
). In addition, UCbase & miRfunc is the first database that provides miRNA function, which is a particularly important feature due to the increasing output of miRNA data. The goal of this study is to offer the researchers an advanced set of tools that supply information about correlation between miRNAs, UCRs and the disorders related to their aberrant expression.
The first version of UCbase & miRfunc includes new methods of queries such as search for band, disorders and genes. It has the capability of using multiple queries and combining the results from several miRNA/UCRs input. In addition, the system has a new tool for the RNA secondary structure prediction (up to 500 bp up/downstream), which allows innovative visualization of miRNAs and ultraconserved elements. This feature improves presentation of data output that is especially useful when several structures are obtained using multiple queries.
The sequence comparison tool, which is also available, allows researchers to match selected sequences that are 500/1000/2000/5000/10 000 bp upstream/downstream of all defined miRNAs and UCRs in the database.
Additionally, UCbase & miRfunc has adopted several strategies to integrate search tools. It provides updated data by using automate web scripts.
The system will be regularly upgraded with new human, mouse and rat miRNAs/UCRs by providing the corresponding reference sequences and annotations, thus allowing the data to be refined continuously with every new miRBase and UCSC database version. It also provides complete human, mouse and rat miRBase table as a single file (available from the resource web page), a feature that is particularly useful if one wants to use regular expressions to identify the segment of the input file associated with sub-field of interest.
Although other alternatives are available for retrieval of miRNA nomenclature, sequence data and annotation, UCbase & miRfunc is unique combination of features that provide biologists many options for data analysis and discovery of relationships between miRNAs and ultraconserved sequences.