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

Pellegrini M, Renda ME, Vecchio A - BMC Bioinformatics (2012)

Bottom Line: We used TReaDS to investigate sequences associated with repeat expansion diseases.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 confirm the specificity of this association.

View Article: PubMed Central - HTML - PubMed

Affiliation: Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy.

ABSTRACT

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 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.

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 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.

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 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.

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Related in: MedlinePlus

TReaDS: example of an algorithm sub-report. The algorithm sub-report of the output report lists separately the tandem repeats found by each algorithm and their basic features.
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Figure 4: TReaDS: example of an algorithm sub-report. The algorithm sub-report of the output report lists separately the tandem repeats found by each algorithm and their basic features.

Mentions: • Algorithm sub-reports. There is one algorithm sub-report for each system included in the search process (see, for instance, Figure 2). It contains the detail of the parameters used and the list of the TRs found by the specific algorithm, including their initial position, length, number of repetitions, and consensus. In case of advanced mode search the parameters are those the user set for the given algorithm, while in case of simple mode search the global parameters given as input are reported (see Figure 4).


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

Pellegrini M, Renda ME, Vecchio A - BMC Bioinformatics (2012)

TReaDS: example of an algorithm sub-report. The algorithm sub-report of the output report lists separately the tandem repeats found by each algorithm and their basic features.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3303744&req=5

Figure 4: TReaDS: example of an algorithm sub-report. The algorithm sub-report of the output report lists separately the tandem repeats found by each algorithm and their basic features.
Mentions: • Algorithm sub-reports. There is one algorithm sub-report for each system included in the search process (see, for instance, Figure 2). It contains the detail of the parameters used and the list of the TRs found by the specific algorithm, including their initial position, length, number of repetitions, and consensus. In case of advanced mode search the parameters are those the user set for the given algorithm, while in case of simple mode search the global parameters given as input are reported (see Figure 4).

Bottom Line: We used TReaDS to investigate sequences associated with repeat expansion diseases.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 confirm the specificity of this association.

View Article: PubMed Central - HTML - PubMed

Affiliation: Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy.

ABSTRACT

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 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.

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 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.

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 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.

Show MeSH
Related in: MedlinePlus