Abstract
MicroRNAs (miRNA) are small non-coding RNA molecules of ∼22 nucleotides which regulate large numbers of genes by binding to seed sequences at the 3′-untranslated region of target gene transcripts. The target mRNA is then usually degraded or translation is inhibited, although thus resulting in posttranscriptional down regulation of gene expression at the mRNA and/or protein level. Due to the bioinformatic difficulties in predicting functional miRNA binding sites, several publically available databases have been developed that predict miRNA binding sites based on different algorithms. The parallel use of different databases is currently indispensable, but highly uncomfortable and time consuming, especially when working with numerous genes of interest. We have therefore developed a new stand-alone program, termed MIRNA-DISTILLER, which allows to compile miRNA data for given target genes from public databases. Currently implemented are TargetScan, microCosm, and miRDB, which may be queried independently, pairwise, or together to calculate the respective intersections. Data are stored locally for application of further analysis tools including freely definable biological parameter filters, customized output-lists for both miRNAs and target genes, and various graphical facilities. The software, a data example file and a tutorial are freely available at http://www.ikp-stuttgart.de/content/language1/html/10415.asp
Highlights
MicroRNAs are single-stranded, non-coding RNA molecules consisting of about 22 nucleotides which generally bind to the 3 -untranslated regions (UTRs) of mRNAs
We have developed MIRNA-DISTILLER, a standalone program which allows to automatically extract selected data for miRNAs predicted to interact with a given set of target genes from several publically available databases
Liver tissues were previously collected from patients undergoing liver surgery at the Department of General, MIRNA-DISTILLER
Summary
MicroRNAs (miRNAs) are single-stranded, non-coding RNA molecules consisting of about 22 nucleotides which generally bind to the 3 -untranslated regions (UTRs) of mRNAs. Www.frontiersin.org there are at least two databases, miRecords and miRò (Laganà et al, 2009; Xiao et al, 2009) which compile miRNA predictions from different databases These tools are useful for some applications, we noticed a lack of practical solutions for the management of large prediction data sets adapted to the needs of the wet-lab researcher. We have developed MIRNA-DISTILLER, a standalone program which allows to automatically extract selected data for miRNAs predicted to interact with a given set of target genes from several publically available databases (in the current version including TargetScan, microCosm, and miRDB). The MIRNA-DISTILLER facilitates miRNA bioinformatics and helps to focus experimental validation on the most promising candidates
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