Abstract

We heuristically derived two new equations for the scale parameter, lambda. This equation can estimate efficiently with high accuracy. In addition, we have proposed several new formulas for Gumbel pre-factor k based on a path reversal identity and the Poisson clumping heuristic. This formula also provides very accurate results. We also have explored edge effects on the statistics. Edge effects are relevant, because real sequences have limited lengths, generating a correction term in an asymptotic expansion of the probability of sequence matching. This edge effect is likely to be more important in the statistics of matching with gaps than it was in the statistics of matching without gaps, because gapped matches tend to be longer, exhausting the sequences being matched more easily. The NCBI CoreTools now has code that calculates all the modified Gumbel parameters to practical accuracies in less than 1 sec. Moreover, the BLAST code now incorporates our improved finite-size correction.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIALM000088-11
Application #
7969220
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
11
Fiscal Year
2009
Total Cost
$82,928
Indirect Cost

  Institution

Name
National Library of Medicine
Department
Type
DUNS #
City
State
Country
Zip Code

  Publications

Gauran, Iris Ivy M; Park, Junyong; Lim, Johan et al. (2018) Empirical null estimation using zero-inflated discrete mixture distributions and its application to protein domain data. Biometrics 74:458-471
Sheetlin, Sergey; Park, Yonil; Frith, Martin C et al. (2016) ALP & FALP: C++ libraries for pairwise local alignment E-values. Bioinformatics 32:304-5
Carroll, Hyrum D; Williams, Alex C; Davis, Anthony G et al. (2015) Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate. IEEE/ACM Trans Comput Biol Bioinform 12:531-7
Sheetlin, Sergey L; Park, Yonil; Frith, Martin C et al. (2014) Frameshift alignment: statistics and post-genomic applications. Bioinformatics :
Park, Yonil; Sheetlin, Sergey; Ma, Ning et al. (2012) New finite-size correction for local alignment score distributions. BMC Res Notes 5:286
Sheetlin, Sergey; Park, Yonil; Spouge, John L (2011) Objective method for estimating asymptotic parameters, with an application to sequence alignment. Phys Rev E Stat Nonlin Soft Matter Phys 84:031914
Park, Yonil; Sheetlin, Sergey; Spouge, John L (2009) ESTIMATING THE GUMBEL SCALE PARAMETER FOR LOCAL ALIGNMENT OF RANDOM SEQUENCES BY IMPORTANCE SAMPLING WITH STOPPING TIMES. Ann Stat 37:3697