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URN: urn:nbn:de:0030-drops-7856
URL: http://drops.dagstuhl.de/opus/volltexte/2006/785/
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Erdös, Péter L. ; Ligeti, Péter ; Sziklai, Péter ; Torney, David C.

Subwords in reverse-complement order

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Abstract

We examine finite words over an alphabet $Gamma={a,bar{a};b,bar{b}}$ of pairs of letters, where each word $w_1w_2...w_t$ is identical with its {it reverse complement} $bar{w_t}...bar{w_2}bar{w_1}$ (where $bar{bbar{a}}=a,bar{bar{b}}=b$). We seek the smallest $k$ such that every word of length $n,$ composed from $Gamma$, is uniquely determined by the set of its subwords of length up to $k$. Our almost sharp result ($ksim 2n/3$) is an analogue of a classical result for ``normal'' words. This classical problem originally was posed by M.P. Sch"utzenberger and I. Simon, and gained a considerable interest for several researchers, foremost by Vladimir Levenshtein. Our problem has its roots in bioinformatics.

BibTeX - Entry

@InProceedings{erds_et_al:DSP:2006:785,
  author =	{P{\'e}ter L. Erd{\"o}s and P{\'e}ter Ligeti and P{\'e}ter Sziklai and David C. Torney},
  title =	{Subwords in reverse-complement order},
  booktitle =	{Combinatorial and Algorithmic Foundations of Pattern and Association Discovery},
  year =	{2006},
  editor =	{Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein},
  number =	{06201},
  series =	{Dagstuhl Seminar Proceedings},
  ISSN =	{1862-4405},
  publisher =	{Internationales Begegnungs- und Forschungszentrum f{\"u}r Informatik (IBFI), Schloss Dagstuhl, Germany},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2006/785},
  annote =	{Keywords: Reverse complement order, Reconstruction of words, Microarray experiments}
}

Keywords: Reverse complement order, Reconstruction of words, Microarray experiments
Seminar: 06201 - Combinatorial and Algorithmic Foundations of Pattern and Association Discovery
Issue Date: 2006
Date of publication: 07.11.2006

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