Asymmetric exclusion process and extremal statistics of random sequences

被引:41
作者
Bundschuh, R [1 ]
机构
[1] Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
来源
PHYSICAL REVIEW E | 2002年 / 65卷 / 03期
关键词
D O I
10.1103/PhysRevE.65.031911
中图分类号
O35 [流体力学]; O53 [等离子体物理学];
学科分类号
070204 ; 080103 ; 080704 ;
摘要
A mapping is established between sequence alignment, one of the most commonly used tools of computational biology, at a certain choice of scoring parameters and the asymmetric exclusion process, one of the few exactly solvable models of nonequilibrium physics. The statistical significance of sequence alignments is characterized through studying the total hopping current of the discrete time and space version of the asymmetric exclusion process.
引用
收藏
页数:19
相关论文
共 47 条
[1]  
Altschul SF, 1996, METHOD ENZYMOL, V266, P460
[2]  
ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999
[3]  
[Anonymous], INTRO COMPUTATIONAL
[4]  
[Anonymous], 1975, J APPL PROBAB
[5]  
[Anonymous], 1978, Atlas of protein sequence and structure
[6]   `A PHASE TRANSITION FOR THE SCORE IN MATCHING RANDOM SEQUENCES ALLOWING DELETIONS [J].
Arratia, Richard ;
Waterman, Michael S. .
ANNALS OF APPLIED PROBABILITY, 1994, 4 (01) :200-225
[7]   An analytic study of the phase transition line in local sequence alignment with gaps [J].
Bundschuh, R ;
Hwa, T .
DISCRETE APPLIED MATHEMATICS, 2000, 104 (1-3) :113-142
[8]  
COLLINS JF, 1988, COMPUT APPL BIOSCI, V4, P67
[9]   Extensive simulations for longest common subsequences - Finite size scaling, a cavity solution, and configuration space properties [J].
de Monvel, JB .
EUROPEAN PHYSICAL JOURNAL B, 1999, 7 (02) :293-308
[10]   Universal large-deviation function of the Kardar-Parisi-Zhang equation in one dimension [J].
Derrida, B ;
Appert, C .
JOURNAL OF STATISTICAL PHYSICS, 1999, 94 (1-2) :1-30