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Tandem Repeats Discovery Service (TReaDS) applied to finding novel Cis-acting factors in Repeat Expansion Diseases

Background: Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion diseases (mostly aff ecting the nervous system). Comparative studies on the output of different tools for finding tandem repeats highlighted significant differences among the sets of detected tandem repeats, while many authors pointed up how critical it is the right choice of parameters.

Results: In this paper we present TReaDS - Tandem Repeats Discovery Service, a tandem repeat meta search engine. TReaDS forwards user requests to several state of the art tools for fi nding tandem repeats and merges their outcome into a single report, providing a global, synthetic, and comparative view of the results. In particular, TReaDS allows the user to (i) simultaneously run diff erent algorithms on the same data set, (ii) choose for each algorithm a di fferent setting of parameters, and (iii) obtain a report that can be downloaded for further, o -line, investigations. We used TReaDS to investigate sequences associated with repeat expansion diseases.

Conclusions: By using the tool TReaDS we discover that, for 27 repeat expansion diseases out of a currently
known set of 29, long fuzzy tandem repeats are covering the expansion loci. Tests with control sets con rm the specifi city of this association. This finding suggests that long fuzzy tandem repeats can be a new class of cis-acting elements involved in the mechanisms leading to the expansion instability.
We strongly believe that biologists can be interested in a tool that, not only gives them the possibility of using multiple search algorithm at the same time, with the same effort exerted in using just one of the systems, but also simpli fies the burden of comparing and merging the results, thus expanding our capabilities in detecting important phenomena related to tandem repeats.


BMC Bioinformatics, 2012

IIT authors:

Alessio Vecchio

Foto di Alessio Vecchio

Type: Article in ISI Journal
Field of reference: Information Technology and Communication Systems
March 2012
Activity: Biologia computazionale