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TReaDS: Tandem Repeats Discovery Service

Tandem Repeats (TRs) are multiple duplications of substrings in the DNA that occur contiguously and may involve mutations, such as substitutions, insertions, and deletions. Not only TRs are privileged targets in activities such as fingerprinting or tracing the evolution of populations, but they have also been linked to several diseases, disorders and addictive behaviors. Even though the depth of the research on TRs has been boosted by the availability of efficient non-trivial algorithms for finding TRs (even when mutations occur with non-negligible probability), comparative studies report significant differences among the sets of TRs that can be detected by using different tools and show how critical it is the choice of the input parameters. Thus, biologists could highly benefit from a tool that gives them the possibility of simultaneously querying multiple systems and getting a global, comparative and synthetic view of the results, with the same effort one would exert in using just one of the systems. Here we present TReaDS, the Tandem Repeats Discovery Service, which allows the user to: simultaneously run different algorithms on the same data set; manually choose for each algorithm a different parameter settings, or express her/his request in a simple and concise way (exact or approximate, short or long TRs), delegating to TReaDS the burden of choosing the right choice of parameters for all the systems; and get back a report that can be also downloaded for further, off-line, investigations. To the best of our knowledge TReaDS is the first meta search engine for tandem repeats and there is no similar and comparable system freely available.

VIII Annual Meeting of the Bioinformatics Italian Society, Pisa, 2011

Autori IIT:

Alessio Vecchio

Foto di Alessio Vecchio

Tipo: Abstract/poster in Atti di convegno internazionale
Area di disciplina: Information Technology and Communication Systems

File: posterRendaBITS2011.pdf