DocumentCode
1989014
Title
The SCP and compressed domain analysis of biological sequences
Author
Adjeroh, Donand ; Feng, Jianan
Author_Institution
Dept. of Comput. Sci. & Electr. Eng., West Virginia Univ., Morgantown, WV, USA
fYear
2003
fDate
11-14 Aug. 2003
Firstpage
587
Lastpage
592
Abstract
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.
Keywords
DNA; biology computing; data compression; molecular biophysics; proteins; anchor points problem; biological sequences; compressed domain analysis; compression schemes; multiple sequence alignment; sorted common prefix; Bioinformatics; Biological system modeling; Compression algorithms; DNA; Data structures; Diseases; Genomics; Humans; Pattern analysis; Sequences;
fLanguage
English
Publisher
ieee
Conference_Titel
Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE
Print_ISBN
0-7695-2000-6
Type
conf
DOI
10.1109/CSB.2003.1227416
Filename
1227416
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