Introduction

The problem of characterizing and detecting over- or under-represented words in sequences arises ubiquitously in diverse applications and has been studied rather extensively in Computational Molecular Biology. In most approaches to the detection of unusual frequencies of words in sequences, the words (up to a certain length) are enumerated more or less exhaustively and individually checked in terms of observed and expected frequencies, variances, and scores of discrepancy and significance thereof. We take instead the global approach of annotating a suffix trie or automaton of a sequence with some such values and scores, with the objective of using it as a collective detector of all unexpected behaviors, or perhaps just as a preliminary filter for words suspicious enough to warrant further and more accurate scrutiny.

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Documentation and Papers

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A.Apostolico, F.Gong, S.Lonardi, "Verbumculus and the Discovery of Unusual Words", Journal of Computer and Science Technology (special issue in Bioinformatics), vol.19, no.1, pp.22-41, 2004. BibTex entry

A.Apostolico, M.E.Bock, S.Lonardi, "Monotony of surprise and large-scale quest for unusual words", to appear in Journal of Computational Biology, July 2003. BibTex entry

A.Apostolico, M.E.Bock, S.Lonardi, "Monotony of surprise and large-scale quest for unusual words", Proceedings of ACM RECOMB, pp.22-31, Washington, DC, 2002. BibTex entry

S.Lonardi, "Global Detectors of Unusual Words: Design, Implementation, and Applications to Pattern Discovery in Biosequences", Ph.D. Thesis, Dept. of Computer Science, Purdue University, August 2001. BibTex entry

Verbumculus user's guide (v1.12)

A.Apostolico, M.E.Bock, S.Lonardi, X.Xu, "Efficient Detection of Unusual Words", Journal of Computational Biology, vol.7, no.1/2, 2000. (jcb.ps.gz, 229,967 bytes; jcb.pdf, 655,877). BibTex entry and PubMed Abstract

A.Apostolico, M.E.Bock, S.Lonardi, "Linear Global Detectors of Redundant and Rare Substrings", Proceeding of the IEEE Data Compression Conference (DCC'99), pp.168-177, Snowbird, Utah, March 29-31, 1999. (dcc99.ps.gz, 100,668 bytes; dcc99.pdf, 332,063). BibTex entry

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Sponsors

Italian Ministry of University and Research (Grant 9905021359/006)

National Science Foundation (Grant CCR-9700276)

Purdue Research Foundation (Grant 690-1398-3145)