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NucBase, an easy to use read mapper for small RNAs

Jeremy Dufourt123, Pierre Pouchin1234, Pierre Peyret5, Emilie Brasset123 and Chantal Vaury123*

Author Affiliations

1 Clermont Université, Université d’Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France

2 Inserm U 1103, F-63001, Clermont-Ferrand, France

3 CNRS, UMR 6293, F-63001, Clermont-Ferrand, France

4 CHRU, F-63001, Clermont-Ferrand, France

5 EA4678, Université d’Auvergne, F-63001, Clermont-Ferrand, France

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Mobile DNA 2013, 4:1  doi:10.1186/1759-8753-4-1

Published: 1 January 2013



High-throughput deep-sequencing technology has generated an unprecedented number of expressed sequence reads that offer the opportunity to get insight into biological systems. Several databases report the sequence of small regulatory RNAs which play a prominent role in the control of transposable elements (TE). However, the huge amount of data reported in these databases remains mostly unexplored because the available tools are hard for biologists to use.


Here we report NucBase, a new program designed to make an exhaustive search for sequence matches and to align short sequence reads from large nucleic acid databases to genomes or input sequences. NucBase includes a graphical interface which allows biologists to align sequences with ease and immediately visualize matched sequences, their number and their genomic position. NucBase identifies nucleic motives with strict identity to input sequences, and it capably finds candidates with one or several mismatches. It offers the opportunity to identify “core sequences” comprised of a chosen number of consecutive matching nucleotides. This software can be run locally on any Windows, Linux or Mac OS computer with 32-bit architecture compatibility.


Since this software is easy to use and can detect reads that were undetected by other software, we believe that it will be useful for biologists involved in the field of TE silencing by small non-coding RNAs. We hope NucBase will be useful for a larger community of researchers, since it makes exploration of small nucleic sequences in any organism much easier.

Alignment; Short reads