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Ww.biomedcentral.com/1471-2105/9/Figure 8 Accumulative indel length distribution Accumulative indel length distribution. The survival function of indel and loop lengths were plotted against a range of lengths from 1 25 residues.idues in comparison to the loops, but less C, I, L, N, P, Q, S, T, V residues. The differences are significant at P value PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/15501003 over a range of indel or loop lengths (from 1?5) was plotted on Figure 8, indicating that there were many short indels/loops but very few longer indels/loops. The number of indels and loops both reduced as the length increased, however, the number of loops reduced as a faster rate than indels. Moreover, the maximal loop length was 26 amino-acid long, while the maximal indel length was 50 in the Indel PDB dataset.Figure 9 tion Indel length modeled by the Weibull and power law distribuIndel length modeled by the Weibull and power law distribution. a) The double logarithm of the survival function in Weibull distribution was plotted against the logarithm of indel length, which ranged from 1 to RRx-001 49 residues. The plot was fitted onto a liner line with R2 = 0.9661, indicating a good fit of the Weibull distribution. b) The logarithm of the survival function in power law distribution was plotted against the logarithm of indel length, which ranged from 1 to 49 residues. The plot was fitted onto a liner line with R2 = 0.9643.power law function. In addition, the results suggest that the occurrence of indels in the studied PDB proteins cannot be attributed to random processes (when normal distribution behaviors would be expected), and the indel lengths are likely to be associated with certain evolutionary mechanisms.Secondary structure composition of indels We have assigned secondary structures to each of the 11,294 indel-containing proteins and their 117,266 indel sites in Indel PDB. Secondary structures were defined and assigned by DSSP [22] and its computer program [21]. Additional file 3 summarizes the secondary structure composition results and the corresponding chi-square and p values of each indel length category, by comparing indel sites and their indel-containing proteins. Figure 11 illustrates that when the indel length increased, there was an increase of alpha-helix content (H) in indels, while the percentages of extended beta-strands (E), H-bonded turns (T), bends (S) and loops decreased. In comparison to the indel proteins (as shown in Figure 12), indel sites have increased percentages of T, S, and loop structures, but reduced contents of alpha helices and beta strands. TheFigure 9a shows a double logarithmic plot of the survival function versus the logarithm of the indel length. The plot could be fitted onto a liner line with R2 value of 0.9661, indicating a good fit of indel length distribution by the Weibull distribution.