Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
A new challenge for compression algorithms: genetic sequences
Information Processing and Management: an International Journal - Special issue: data compression
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
Estimating DNA sequence entropy
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
Significantly Lower Entropy Estimates for Natural DNA Sequences
DCC '97 Proceedings of the Conference on Data Compression
DNA Sequence Compression Using the Burrows-Wheeler Transform
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Locating All Tandem Repeat Families in a Sequence
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
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We introduce the SCP - the sortedcommon prefix, and study some of its properties.Based on the internal representations used by aclass of new compression schemes, we show howthe SCP table can be constructed using anO(u + |Sigma|\kappamax) number of comparisons onaverage, and O(u|\Sigma|) worst case, where u is thesize of the sequence, |\Sigma| is the number of symbols,and \kappmax is the maximum SCP value.Wedescribe one application of the SCP to the problemof anchor points in multiple sequence alignment.