Limits...
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.

Show MeSH

Related in: MedlinePlus

A cluster returned in graphical format. Example of a cluster returned by TReaDS: the cluster is showed in a graphical format, with the original sequence opportunely underlined in the position of the found TR, and with different colors, each corresponding to the particular queried algorithm returning the TR.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3303744&req=5

Figure 6: A cluster returned in graphical format. Example of a cluster returned by TReaDS: the cluster is showed in a graphical format, with the original sequence opportunely underlined in the position of the found TR, and with different colors, each corresponding to the particular queried algorithm returning the TR.

Mentions: • Clusters sub-report. TReaDS merges the results of all algorithms to give a global view of them by identifying overlapping TRs. Two TRs overlap if they share one or more positions in the sequence. The overlapping relation is an equivalence relation thus it allows us to partition the found TRs into groups that we call clusters. Such clusters are reported in the clusters sub-report (see Figure 5). Graphically, a cluster covers a contiguous segment of the input sequence without gaps. The report contains a list of all clusters found. For each cluster the following information is included: flanking sequence (if requested), starting and ending positions of the covered segment, list of TRs that form the cluster, and some details for each TR (starting and ending position, length, number of repetitions, consensus). If the user has chosen to include the images in the final report, it is also possible to view each cluster in a graphical form (see Figure 6).


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)

A cluster returned in graphical format. Example of a cluster returned by TReaDS: the cluster is showed in a graphical format, with the original sequence opportunely underlined in the position of the found TR, and with different colors, each corresponding to the particular queried algorithm returning the TR.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: A cluster returned in graphical format. Example of a cluster returned by TReaDS: the cluster is showed in a graphical format, with the original sequence opportunely underlined in the position of the found TR, and with different colors, each corresponding to the particular queried algorithm returning the TR.
Mentions: • Clusters sub-report. TReaDS merges the results of all algorithms to give a global view of them by identifying overlapping TRs. Two TRs overlap if they share one or more positions in the sequence. The overlapping relation is an equivalence relation thus it allows us to partition the found TRs into groups that we call clusters. Such clusters are reported in the clusters sub-report (see Figure 5). Graphically, a cluster covers a contiguous segment of the input sequence without gaps. The report contains a list of all clusters found. For each cluster the following information is included: flanking sequence (if requested), starting and ending positions of the covered segment, list of TRs that form the cluster, and some details for each TR (starting and ending position, length, number of repetitions, consensus). If the user has chosen to include the images in the final report, it is also possible to view each cluster in a graphical form (see Figure 6).

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