References

[1]
D. J. Zea, D. Anfossi, M. Nielsen and C. Marino-Buslje. MIToS. jl: mutual information tools for protein sequence analysis in the Julia language. Bioinformatics 33, 564–565 (2017).
[2]
U. Hobohm, M. Scharf, R. Schneider and C. Sander. Selection of representative protein data sets. Protein Science 1, 409–417 (1992).
[3]
C. M. Buslje, J. Santos, J. M. Delfino and M. Nielsen. Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. Bioinformatics 25, 1125–1131 (2009).
[4]
S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller and D. J. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25, 3389–3402 (1997).
[5]
S. D. Dunn, L. M. Wahl and G. B. Gloor. Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics 24, 333–340 (2008).
[6]
S. Velankar, J. M. Dana, J. Jacobsen, G. van Ginkel, P. J. Gane, J. Luo, T. J. Oldfield, C. O’Donovan, M.-J. Martin and G. J. Kleywegt. SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Research 41, D483-D489 (2012).
[7]
P. Stothard. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28, 1102–1104 (2000).
[8]
B. J. Grant, A. P. Rodrigues, K. M. ElSawy, J. A. McCammon and L. S. Caves. Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics 22, 2695–2696 (2006).
[9]
W. Perks. Some observations on inverse probability including a new indifference rule. Journal of the Institute of Actuaries 73, 285–334 (1947).
[10]
S. Trybula. Some problems of simultaneous minimax estimation. The Annals of Mathematical Statistics 29, 245–253 (1958).
[11]
H. Jeffreys. An invariant form for the prior probability in estimation problems. Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences 186, 453–461 (1946).
[12]
C. Marino Buslje, E. Teppa, T. Di Doménico, J. M. Delfino and M. Nielsen. Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification. PLoS computational biology 6, e1000978 (2010).