Additional file 1: of TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs

Supplementary materials. This file contains details of splicing graph construction, additional comparisons with other methods, and supplementary figures and tables. (PDF 7353 kb

Protein sectors of G protein family (A and B) and Hsp70/110 family (C and D).

<p>Red balls and Green balls represent different protein sectors in protein 3D structure. Residues comprising protein sectors are displayed in space filling representation with a van der Waals surface.</p

The performance of BIFANR on original data and half data in S1A family.

<p>The performance of BIFANR on original data and half data in S1A family.</p

Average correlation coefficients of protein sectors.

<p>A: Average correlation coefficient of each protein sector in S1A family. B: Average correlation coefficient of each protein sector in PDZ family. Red column represents average correlation coefficient of protein sector 1. Blue column represents average correlation coefficient of protein sector 2. Green column represents average correlation coefficient of protein sector 3. Black column represents stochastic expected average correlation coefficient of each protein sector.</p

Bi-Factor Analysis Based on Noise-Reduction (BIFANR): A New Algorithm for Detecting Coevolving Amino Acid Sites in Proteins

<div><p>Previous statistical analyses have shown that amino acid sites in a protein evolve in a correlated way instead of independently. Even though located distantly in the linear sequence, the coevolved amino acids could be spatially adjacent in the tertiary structure, and constitute specific protein sectors. Moreover, these protein sectors are independent of one another in structure, function, and even evolution. Thus, systematic studies on protein sectors inside a protein will contribute to the clarification of protein function. In this paper, we propose a new algorithm BIFANR (Bi-factor Analysis Based on Noise-reduction) for detecting protein sectors in amino acid sequences. After applying BIFANR on S1A family and PDZ family, we carried out internal correlation test, statistical independence test, evolutionary rate analysis, evolutionary independence analysis, and function analysis to assess the prediction. The results showed that the amino acids in certain predicted protein sector are closely correlated in structure, function, and evolution, while protein sectors are nearly statistically independent. The results also indicated that the protein sectors have distinct evolutionary directions. In addition, compared with other algorithms, BIFANR has higher accuracy and robustness under the influence of noise sites.</p></div

Comparison between BIFANR and Buck’s in S1A family.

<p>A: S1,S2, and S3 represent 3 experimental confirmed protein sectors in S1A family and the height of color bar represents the number of sites in corresponding predicted protein sector by Buck’s method. B: S1,S2, and S3 represent 3 protein sectors in S1A family and the height of each color bar represents the number of sites in corresponding predicted sector by BIFANR. And the height of the brown bar represents the number of lost sites by algorithms in each experimental confirmed protein sector.</p

Evolutionary independence of protein sectors in S1A family.

<p>A: Evolutionary independence of protein sector 1. B: Evolutionary independence of protein sector 2. C: Evolutionary independence of protein sector 3.</p

Average evolutionary rate of each protein sector and average evolutionary rate of all sites in S1A and PDZ.

<p>Average evolutionary rate of each protein sector and average evolutionary rate of all sites in S1A and PDZ.</p

Distribution of amino acid site evolutionary rates.

<p>A: Distribution of amino acid site evolutionary rates in S1A family (rat trypsin: 3TGI). B: Distribution of amino acid site evolutionary rates in PDZ family (rat PSD-95∶1BE9). Red column represents the evolutionary rate distribution of amino acid sites in protein sectors.</p

Statistical independence of protein sectors.

<p>A: Statistical independence of protein sectors in S1A family. B: Statistical independence of protein sectors in PDZ family. (Red column represents MDI entropy of protein sector 1. Blue column represents MDI entropy of protein sector 2. Green column represents MDI entropy of protein sector 3. Black column represents MDI entropy of two protein sectors as a whole. Yellow column represents stochastic expected MDI entropy after disrupting the amino acid sites within two protein sectors 100 times.).</p