Concepedia

Gap Penalty Optimization

Gap Penalty Optimization is a computational method in sequence alignment that determines the optimal values for gap penalties by balancing the trade-off between alignment accuracy and biological plausibility, distinguishing it from other alignment strategies through its focus on systematically refining gap cost parameters to enhance global or local homology inference.

39

Publications

4.5K

Citations

88

Authors

53

Institutions

Publications per year

2017–2026

4

Parents

Publications

39

Optimal alignments in linear space

Eugene W. Myers, Webb Miller · Computer applications in the biosciences · 1988 · 1.2K citations

, , +13

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties11Edited by B. Honig

Jiye Shi, Tom L. Blundell, Kenji Mizuguchi · Journal of Molecular Biology · 2001 · 1.2K citations

, , +11

Optimal sequence alignment using affine gap costs

Stephen F. Altschul, Bruce W. Erickson · Bulletin of Mathematical Biology · 1986 · 232 citations

, , +9

A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given.

Jotun Hein · Molecular Biology and Evolution · 1989 · 182 citations · Full text

, , +17

The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment

Xun Gu, Wen‐Hsiung Li · Journal of Molecular Evolution · 1995 · 160 citations

, , +17

1–5 of 39

Authors

88

  1. SF
    Stephen F. Altschul

    National Institutes of Health, United States

    3 publications · 436 citations

    3

    h-index

  2. HZ
    Haowen Zhang

    Georgia Institute of Technology, United States

    2 publications · 52 citations

    2

    h-index

  3. OG
    Osamu Gotoh

    Saitama Cancer Center, Japan

    2 publications · 171 citations

    2

    h-index

  4. ML
    Michael L. Fredman

    University of California San Diego, United States

    2 publications · 71 citations

    2

    h-index

  5. YG
    Yu Gao

    Georgia Institute of Technology, United States

    2 publications · 52 citations

    2

    h-index

1–5 of 88

Institutions

53

  1. Saitama Cancer Center

    Saitama, Japan

    2 h-index

    2 publications

    171 citations

  2. Monash University

    Melbourne, Australia

    2 h-index

    4 publications

    77 citations

  3. The University of Texas at Austin

    Austin, United States

    2 h-index

    8 publications

    233 citations

  4. Georgia Institute of Technology

    Atlanta, United States

    2 h-index

    8 publications

    208 citations

  5. University of California San Diego

    San Diego, United States

    2 h-index

    2 publications

    71 citations

  6. University of Wisconsin–Madison

    Madison, United States

    2 h-index

    2 publications

    80 citations

  7. University of Arizona

    Tucson, United States

    2 h-index

    6 publications

    1.3K citations

  8. National Institutes of Health

    Bethesda, United States

    1 h-index

    1 publications

    22 citations

1–8 of 53

Venues

  1. Bulletin of Mathematical Biology

    6 publications · 538 citations

    6

    h-index

  2. Protein Engineering Design and Selection

    PEDS · 3 publications · 206 citations

    3

    h-index

  3. Journal of Theoretical Biology

    3 publications · 173 citations

    3

    h-index

  4. Journal of Molecular Biology

    JMB · 2 publications · 1.3K citations

    2

    h-index

  5. Molecular Biology and Evolution

    MBE · 2 publications · 198 citations

    2

    h-index

1–5