Esko Ukkonen

On-line construction of suffix trees

An on-line algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. The new algorithm has the desirable property of processing the string symbol by symbol from left to right. It always has the suffix tree for the scanned part of the string ready. The method is developed as a linear-time version of a very simple algorithm for (quadratic size) suffixtries. Regardless of its quadratic worst case this latter algorithm can be a good practical method when the string is not too long. Another variation of this method is shown to give, in a natural way, the well-known algorithms for constructing suffix automata (DAWGs).

DNA-binding specificities of human transcription factors.

Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificities. The models represent the majority of human TFs, approximately doubling the coverage compared to existing systematic studies. Our results reveal additional specificity determinants for a large number of factors for which a partial specificity was known, including a commonly observed A- or T-rich stretch that flanks the core motifs. Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated. We further describe a binding model incorporating these features that is required to understand binding of TFs to DNA.

Approximate string-matching with q -grams and maximal matches

We study approximate string matching in connection with two string distance functions that are computable in linear time. The first function is based on the so-called

Algorithms for approximate string matching

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The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

-grams. An algorithm is given for the associated string matching problem that finds the locally best approximate occurences of pattern

Finding approximate patterns in strings

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Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

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A global map of human gene expression

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Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

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Two algorithms for approxmate string matching in static texts

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