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The SCP and compressed domain analysis of biological sequences

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2 Author(s)
Adjeroh, D. ; Dept. of Comput. Sci. & Electr. Eng., West Virginia Univ., Morgantown, WV, USA ; Feng, J.

We introduce the SCP - the sorted common prefix, and study some of its properties. Based on the internal representations used by a class of new compression schemes, we show how the SCP table can be constructed using an O(u+| Σ |Kmax) number of comparisons on average, and O(u | Σ |) worst case, where u is the size of the sequence, | Σ | is the number of symbols, and Kmax is the maximum SCP value. We describe one application of the SCP to the problem of anchor points in multiple sequence alignment.

Published in:

Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE

Date of Conference:

11-14 Aug. 2003