Distribution of indel lengths

Qian, B Goldstein, RA

B. Qian et Ra. Goldstein, Distribution of indel lengths, PROTEINS, 45(1), 2001, pp. 102-104

11

INGLESE

Article

Biochemistry & Biophysics

PROTEINS-STRUCTURE FUNCTION AND GENETICS

0887-3585 → ACNP

45

1

2001

102 - 104

ISI

0887-3585(20011001)45:1<102:DOIL>2.0.ZU;2-W

Protein sequence alignment has become a widely used method in the study of newly sequenced proteins. Most sequence alignment methods use an affine gap penalty to assign scores to insertions and deletions. Although affine gap penalties represent the relative ease of extending a gap compared with init ializing a gap, it is still an obvious oversimplification of the real proce sses that occur during sequence evolution. To improve the efficiency of seq uence alignment methods and to obtain a better understanding of the process of sequence evolution, we wanted to find a more accurate model of insertio ns and deletions in homologous proteins. In this work, we extract the proba bility of a gap occurrence and the resulting gap length distribution in dis tantly related proteins (sequence identity < 25%) using alignments based on their common structures. We observe a distribution of gaps that can be fit ted with a multiexponential with four distinct components. The results sugg est new approaches to modeling insertions and deletions in sequence alignme nts. (C) 2001 Wiley-Liss, Inc.