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Bioinformatics
Article . 2003 . Peer-reviewed
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Bioinformatics
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Bioinformatics
Article . 2004
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Article . 2003
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STRING: finding tandem repeats in DNA sequences

Authors: ALUFFI PENTINI, Filippo; PARISI, Valerio; V. De Fonzo;

STRING: finding tandem repeats in DNA sequences

Abstract

Abstract Motivation and results: The importance of Tandem Repeats in some genomes is now well established. We have reported elsewhere some interesting new results obtained by means of a preliminary program for finding Tandem Repeats in DNA sequences, together with a brief description of the basic ideas of the algorithm. We describe here a completely new program based only in part on those ideas, we briefly discuss the interpretation of the results, and, by way of example, we provide a few novel results relative to the parasites responsible of two re-emerging diseases, Plasmodium falciparum and Mycobacterium tuberculosis. Our program is portable, effective, powerful and fast: it can run on current desktop computers, and it finds all significant Tandem Repeats also in the longest segments of sequences in databases (up to millions of bases), in short times (minutes). Availability: An academic version of the algorithm (full source listing in standard C language) can be freely downloaded (http://www.caspur.it/~castri/STRING/). Supplementary information: Some illustrative figures and some sample results are provided as supplementary material at: http://www.caspur.it/~castri/STRING/

Country
Italy
Keywords

Genome, Base Sequence, Gene Expression Profiling, Molecular Sequence Data, Plasmodium falciparum, Mycobacterium tuberculosis, Sequence Analysis, DNA, Tandem Repeat Sequences, Animals, Databases, Nucleic Acid, Genome, Protozoan, Sequence Alignment, Algorithms, Genome, Bacterial, Software

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    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
48
Top 10%
Top 10%
Top 10%
gold