Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases

BMC Bioinformatics 2012, 13(Suppl 4):S3 doi:10.1186/1471-2105-13-S4-S3

Marco Pellegrini 1, Maria Elena Renda 1 and Alessio Vecchio 2
1 Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy
2 Dipartimento di Ingegneria dell'Informazione, Università di Pisa, Pisa I-56122, Italy

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Fuzzy tandem repeats as potential cis-regulatory elements in repeat expansion disorders

In [14] we noticed that the locus associated with the unstable trinucleotide repeat in the Frataxin protein mRNA coding sequence (whose abnormal expansion is cause of Frederich's ataxia) was included in a much longer fuzzy TR, detected using the proposed TRStalker system.

The present research originated from the hypothesis that this fact (a long fuzzy TR covering the unstable locus) could be observed in a large number of trinucleotide repeat disorders. Consequently, FTR could be exposed as a novel cis-regulatory element not yet studied in literature.

We employ the tool TReaDS in order to quickly collect and organize the output of several TR finding algorithms into a single easy to read report in support to this hypothesis.