Measures relating word frequencies and expectations have been constantly ofinterest in Bioinformatics studies. With sequence data becoming massively available, exhaustiveenumeration of such measures have become concei...Measures relating word frequencies and expectations have been constantly ofinterest in Bioinformatics studies. With sequence data becoming massively available, exhaustiveenumeration of such measures have become conceivable, and yet pose significant computational burdeneven when limited to words of bounded maximum length. In addition, the display of the huge tablespossibly resulting from these counts poses practical problems of visualization and inference.VERBUMCULUS is a suite of software tools for the efficient and fast detection of over- orunder-represented words in nucleotide sequences. The inner core of VERBUMCULUS rests on subtlyinterwoven properties of statistics, pattern matching and combinatorics on words, that enable one tolimit drastically and a priori the set of over-or under-represented candidate words of all lengthsin a given sequence, thereby rendering it more feasible both to detect and visualize such words in afast and practically useful way. This paper is devoted to the description of the facility at theoutset and to report experimental results, ranging from simulations on synthetic data to thediscovery of regulatory elements on the upstream regions of a set of genes of the yeast.展开更多
基金美国自然科学基金，Purdue Research Foundation，Italian Ministry of University and Research, and the Research Program of the University of Padova 及Purdue Research Foundation，the Italian Ministry of University and Re-search, the Research Program of the University of Padova and Bourns College of Engineering, University of California,Riverside
文摘Measures relating word frequencies and expectations have been constantly ofinterest in Bioinformatics studies. With sequence data becoming massively available, exhaustiveenumeration of such measures have become conceivable, and yet pose significant computational burdeneven when limited to words of bounded maximum length. In addition, the display of the huge tablespossibly resulting from these counts poses practical problems of visualization and inference.VERBUMCULUS is a suite of software tools for the efficient and fast detection of over- orunder-represented words in nucleotide sequences. The inner core of VERBUMCULUS rests on subtlyinterwoven properties of statistics, pattern matching and combinatorics on words, that enable one tolimit drastically and a priori the set of over-or under-represented candidate words of all lengthsin a given sequence, thereby rendering it more feasible both to detect and visualize such words in afast and practically useful way. This paper is devoted to the description of the facility at theoutset and to report experimental results, ranging from simulations on synthetic data to thediscovery of regulatory elements on the upstream regions of a set of genes of the yeast.
