Abstract
BackgroundTandem 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 affecting 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.ResultsIn 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 finding 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 different algorithms on the same data set, (ii) choose for each algorithm a different setting of parameters, and (iii) obtain a report that can be downloaded for further, off-line, investigations. We used TReaDS to investigate sequences associated with repeat expansion diseases.ConclusionsBy 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 confirm the specificity 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 simplifies the burden of comparing and merging the results, thus expanding our capabilities in detecting important phenomena related to tandem repeats.
Highlights
Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations
Experimental methodology The relevant sequences have been downloaded from PubMed (See NCBI codes in Additional file 1) and the position of the expansion locus identified via reference to the relevant literature for the target disease
The tool TReaDS has been set with 5 algorithms; the parameter setting is reported in table 4
Summary
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 for their association with the class of repeat expansion diseases (mostly affecting the nervous system). Overview on repeat expansion diseases At present 29 diseases are classified as repeat expansion diseases (RE) [1,2,3], and the number is growing. These are mostly neurodegenerative and neuromuscolar disorders, including Huntington disease (HD), Kennedy disease (SBMA), and several types of Spinocerebral Ataxias (SCA). Since up to recently all known cases involved repeating a motif of 3 nucleotides, this class was denoted as trinucleotide repeat (TNR) expansion disease. Two main questions are related to the study of these diseases from a genetic point of view: (a) which mechanisms or conditions lead to the repeat expansion? and (b) how do repeat expansions result in diseases?
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