Name
Abstract | ||
|---|---|---|
Imposing constraints is an effective means to incorporate biological knowledge into alignment procedures. As in the PROSITE
database, functional sites of proteins can be effectively described as regular expressions. In an alignment of protein sequences
it is natural to expect that functional motifs should be aligned together. Due to this motivation, in CPM 2005 Arslan introduced
the regular expression constrained sequence alignment problem and proposed an algorithm which can take time and space up to
O(|Σ|2 |V|4
n
2) and O(|Σ|2 |V|4
n), respectively, where Σ is the alphabet, n is the sequence length, and V is the set of states in an automaton equivalent to the input regular expression. In this paper we propose a more efficient
algorithm solving this problem which takes O(|V|3
n
2) time and O(|V|2
n) space in the worst case. If |V|=O(logn) we propose another algorithm with time complexity O(|V|2log|V| n
2). The time complexity of our algorithms is independent of Σ, which is desirable in protein applications where the formulation
of this problem originates; a factor of |Σ|2 = 400 in the time complexity of the previously proposed algorithm would significantly affect the efficiency in practice.
|
Year | DOI | Venue |
|---|---|---|
2007 | 10.1016/j.ipl.2007.04.007 | Information Processing Letters |
Keywords | DocType | Volume |
alignment procedure,input regular expression,time complexity o,functional site,protein application,functional motif,efficient algorithm,regular expression,sequence alignment problem,time complexity,sequence alignment,protein sequence,algorithms,database systems,computational complexity,proteins,pattern matching | Journal | 103 |
Issue | ISSN | ISBN |
6 | 0020-0190 | 3-540-35455-7 |
Citations | PageRank | References |
6 | 0.45 | 12 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Yun-Sheng Chung | 1 | 20 | 1.84 |
| Chin Lung Lu | 2 | 423 | 34.59 |
| Chuan Yi Tang | 3 | 704 | 79.25 |