The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment.
The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment.
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DOI：
10.1093/nar/gki800
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发表时间：
2005
影响因子：
14.9
通讯作者：
Spouge JL
中科院分区：
文献类型：
--
作者：
Sheetlin S;Park Y;Spouge JL
The optimal gapped local alignment score of two random sequences follows a Gumbel distribution. The Gumbel distribution has two parameters, the scale parameter λ and the pre-factor k. Presently, the basic local alignment search tool (BLAST) programs (BLASTP (BLAST for proteins), PSI-BLAST, etc.) use all time-consuming computer simulations to determine the Gumbel parameters. Because the simulations must be done offline, BLAST users are restricted in their choice of alignment scoring schemes. The ultimate aim of this paper is to speed the simulations, to determine the Gumbel parameters online, and to remove the corresponding restrictions on BLAST users. Simulations for the scale parameter λ can be as much as five times faster, if they use global instead of local alignment [R. Bundschuh (2002) J. Comput. Biol., 9, 243–260]. Unfortunately, the acceleration does not extend in determining the Gumbel pre-factor k, because k has no known mathematical relationship to global alignment. This paper relates k to global alignment and exploits the relationship to show that for the BLASTP defaults, 10 000 realizations with sequences of average length 140 suffice to estimate both Gumbel parameters λ and k within the errors required (λ, 0.8%; k, 10%). For the BLASTP defaults, simulations for both Gumbel parameters now take less than 30 s on a 2.8 GHz Pentium 4 processor.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
5.8
作者：
Mott, R
通讯作者：
Mott, R
影响因子：
1.8
作者：
Arratia, Richard;Waterman, Michael S.
通讯作者：
Waterman, Michael S.
影响因子：
1.7
作者：
Bundschuh, R
通讯作者：
Bundschuh, R
影响因子：
4.5
作者：
HUBER, PJ
通讯作者：
HUBER, PJ