TReaDS - Tandem Repeats Discovery Service
TReaDS - Tandem Repeats Discovery Service is a tandem repeat meta search engine, aiming to provide users with a wide range of on line available algorithms for finding exact, approximate, short and long tandem repeats.
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TReaDS allows you to:
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simultaneously run different algorithms on the same data sets
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for each algorithm chose different parameter setting
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get the results of each algorithm as a report, in which a comparison page of all results is also included
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download or receive via email the reports for further, off-line, investigations
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Please, send any comments, bug reports, opinions to:
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How to use TReaDS
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The on line available algorithms for finding tandem repeats currently supported by TReaDS are:
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You can select any combination of the supported tools, and give the kind of tandem repeats you are looking for
(in the simple mode parameter setting) or change the parameter settings for each of the selected tools
(in the advanced mode parameter setting). A help window will pop-up on your request to
explain the parameters.
You can also decide to include (all of part of) the input sequence in the report,
or to omit it, and the flanking sequence (up to 200bp).
At last, you can upload either a FASTA or plain text genomic sequence
(as a file, or past the sequence in a given text area), or try one of the provided
example sequences. Note that multi-fasta format is not supported.
TReaDS pre-processes the input sequence in order to (i) remove spaces, numbers, CR and LF characters, (ii) check that all characters belong to the set of allowed characters, and (iii) verify if the sequence is acceptable according to the systems policies (if it not for a given system, that system will not be queried and the motivation will be reported in the summary subsection of the report).
Note: TReaDS' upload size has been fixed to 2MB.
This is because ATRHunter version available on-line allows uploads of sequences up to 2 millions bp large.
TReaDS simultaneously query the selected tools, merges the results obtained, and generates a final report, containing:
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a header page, with date and time of the request;
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a summary report of the sequence submitted, reporting the sequence length, the A, C, G, T, N's percentage, and
the sequence itself (or part of it), if requested;
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a summary report of the tols queried, reporting the algorithm name, the number of tandem repeats found,
whether the connection with the server has been successful, and its response time;
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for each tool, a page titled with the tool name, reporting the input parameter setting chosen, and the list of the TR found, containing the
tandem repeat initial position, the tandem repeat length, the number of times it was repeated,
and the tandem repeat itself;
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a global page reporting the tandem repeats found, clustered basing on their position in the sequence.
TReaDS merges the results of all algorithms to give a global view of them by identifying TRs
with some overlaps. Formally, the overlap relationship among TRs induces a graph, and a cluster is a connected component of this graph.
Graphically, a cluster covers a contiguous segment of the input sequence without gaps.
In this cluster list, for each cluster it is reported the
starting and end position of the tandem repeats it contains, and for each TR in the cluster its start position, its
end position, its length, the number of repetitions, the algorithm responsible for it, and the TR itself. It is
also possible to view, for each cluster, the correspondent segment of the input sequence, where a different colored
and shaped line is associated with each tool, and the positions of the TRs found are indicated by a colored
segment. Note that the report includes the flanking sequence in every cluster
(and its lenght is a parameter to set in the main page).
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References:
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Tandem Repeats Discovery Service (TReaDS) applied to finding novel Cis-acting factors in Repeat Expansion Diseases
Marco Pellegrini, M. Elena Renda, Alessio Vecchio
BMC Bioinformatics 2012, Vol. 13(Suppl 4):S3, March 2012.
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TReaDS: Tandem Repeats Discovery Service
M. Elena Renda, Alessio Vecchio, Marco Pellegrini
VIII Annual Meeting of the Bioinformatics Italian Society (BITS'11), pp 102-104. Pisa, Italy, June 2011.
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TRStalker: an Efficient Heuristic for Finding Fuzzy Tandem Repeats
Marco Pellegrini, M. Elena Renda, Alessio Vecchio
Bioinformatics. Published by Oxford University Press, Volume 26, Issue 12, pp i358-i366. June 2010. doi: 10.1093/bioinformatics/btq209.
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Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression
Valentina Boeva, Mireille Regnier, Dmitri Papatsenko, and Vsevolod Makeev
Bioinformatics, Vol. 22, Issue 6, pp 676-684, 2006.
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Finding Approximate Tandem Repeats in Genomic Sequences
Ydo Wexler, Zohar Yakhini, Yechezkel Kashi and Dan Geiger
International Conference on Research in Computational Molecular Biology (Recomb), 2004.
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mreps: efficient and flexible detection of tandem repeats in DNA
R. Kolpakov, G. Bana, and G. Kucherov
Nucleic Acid Research, Vol. 31, Issue 13, pp 3672-3678, 2003.
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Tandem repeats finder: a program to analyze DNA sequences
G. Benson
Nucleic Acids Research Vol. 27, Issue 2, pp 573-580, 1999.
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