Research references

Chou PY and Fasman GD (1978). "Prediction of the secondary structure of proteins from their amino acid sequence." Advances in Enzymology 47: 45-148.

Darling AE, Mau B, and Perna NT (2010). “progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss, and Rearrangement.” PLoS One. 5(6):e11147. (See the PLOS ONE entry.)

Dayhoff MO, Schwartz R and Orcutt BC (1978). “A model of evolutionary change in proteins”. Atlas of protein sequence and structure (volume 5, supplement 3 ed.). Nat. Biomed. Res. Found. pp. 345–358. ISBN 0-912466-07-3.

Deléage G and Roux B (1987). "An algorithm for protein secondary structure prediction based on class prediction." Protein Engineering 1: 289-294.

Edgar RC (2004). “MUSCLE: multiple sequence alignment with high accuracy and high throughput.” Nucleic Acids Res. 32(5):1792-1797. (See the PubMed entry).

Edgar RC (2004). “MUSCLE: a multiple sequence alignment method with reduced time and space complexity.” BMC Bioinformatics (5):113 (See the PubMed entry).

Eisenberg D, Weiss RM and Terwilliger TC (1984). "The hydrophobic moment detects periodicity in protein hydrophobicity." Proceedings of the National Academy of Science (USA), 81(1): 140-144.

Garnier J, Gibrat JF, Robson B (1996). "GOR method for predicting protein secondary structure from amino acid sequence." Methods Enzymol. 266:540-53. [Reference pertains to MegAlign Pro’s GOR IV algorithm].

Garnier J, Osguthorpe DJ and Robson B (1978). "Analysis of the accuracy and implications of simple method for predicting the secondary structure of globular proteins." Journal of Molecular Biology, 120: 97-120. [Reference pertains to MegAlign Pro’s Garnier-Robson method].

Garnier J and Robson B (1990). "The GOR Method for Predicting Secondary Structures in Proteins." In Prediction of Protein Structure and the Principles of Protein Conformation, ed. G.D. Fasman (2nd ed). Plenum Press, New York. [Reference pertains to MegAlign Pro’s GOR II algorithm].

Gascuel O (1997). “ BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.” Molecular Biology and Evolution 14:685-695. (See the PubMed entry.) [[MegAlign Pro’s tree-building algorithm]

Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD and Bairoch A (2005). "Protein Identification and Analysis Tools on the ExPASy Server." In The Proteomics Protocols Handbook, ed. John M. Walker, Humana Press, pp. 571-607.

Guruprasad K, Reddy BVB and Pandit MW (1990). "Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence." Protein Eng., 4, 155 – 161.

Henikoff S & Henikoff JG (1992). “Amino Acid Substitution Matrices from Protein Blocks”. PNAS. 89 (22): 10915–10919. (See the PubMed entry)

Hopp TP and Woods KR (1981). "Prediction of protein antigenic determinants from amino acid sequences." Proceedings of the National Academy of Science, 78: 3824-3828.

Jameson BA and Wolf H (1988). "The antigenic index: a novel algorithm for predicting antigenic determinants." CABIOS, 4: 181-186.

Kabsch W and Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features." Biopolymers, 22: 2577-2637.

Katoh M, Kumar M (2002) “MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.” (Nucleic Acids Res. 30:3059-3066).

Kimura M (1980). “A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.” J. Mol. Evol., 16: 111-120.

Kimura M (1983). The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.

Kozlov AM, Darriba D, Flouri T, Morel B, Stamataki A (2019). “RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.” Bioinformatics, Volume 35, Issue 21, November 2019, Pages 4453–4455. https://doi.org/10.1093/bioinformatics/btz305

Kyte J, Doolittle RF. (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol., 157, 105-132. [Hydrophobicity color scheme ]

Lehninger A (2005). Principles of Biochemistry, 4th Edition, Chapter 3, page 78, Table 3-1.

Lehninger A, Nelson D, and Cox M (2005). “Principles of biochemistry.” New York: W.H. Freeman.

Müller T, Spang R, Vingron M (2002). “Estimating amino acid substitution models: a comparison of Dayhoff’s estimator, the resolvent approach and a maximum likelihood method.” Mol Biol Evol. 2002 Jan;19(1):8-13. (See the PubMed entry)

Müller T & Vingron (2000). “Modeling amino acid replacement.” J Comput Biol. 2000;7(6):761-76. (See the PubMed entry)

Nakashima H, Nishikawa K and Ooi T (1986). “The folding type of a protein is relevant to the amino acid composition.” Journal of Biochemistry (Tokyo), 99: 153-162.

Nguyen LT, Schmidt HA, von Haeseler A, Quang Minh B (2015). “IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies.” Molecular Biology and Evolution, Volume 32, Issue 1, January 2015, Pages 268–274, https://doi.org/10.1093/molbev/msu300

Nishino, Kunihiko & Yamasaki, Seiji & Hayashi-Nishino, Mitsuko & Yamaguchi, Akihito. (2010). “Effect of NlpE Overproduction on Multidrug Resistance in Escherichia coli.” Antimicrobial agents and chemotherapy. 54. 2239-43. 10.1128/AAC.01677-09. [ View on PubMed ]

Parker JMR, Guo D and Hodges RS (1986). “New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: Correlation of predicted surface residues with antigenicity and x-ray-derived accessible sites.” Biochemistry, 25: 5425-5432.

Saito N and Nei M (1987). “The neighbor-joining method: a new method for reconstructing phylogenetic trees.” Mol Biol Evol. 1987 Jul;4(4):406-25.

Schneider TD and Stephens RM (1990). “Sequence logos: a new way to display consensus sequences.” Nucleic Acids Research, 18 (20): 6097-6100 doi:10.1093/nar/18.20.6097. (See the PubMed entry) [Sequence Logo track]

Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins D (2011). “Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.” Molecular Systems Biology 7, Article number: 539 (See the article in Nature)

Sonnhammer ELL and Hollich V (2005). “Scoredist: A simple and robust protein sequence distance estimator.” BMC Bioinformatics 2005, 6:108. (See on Biomed Central.) [Scoredist model]

Stamatakis A (2014). “RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies”. Bioinformatics, 2014. [RAxML tree-building algorithm]

Tamura K and Nei M (1993). “Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.” Mol Biol Evol. 1993 May;10(3):512-26.

Taylor WR (1997). “Residual colours: a proposal for aminochromography.” Protein Engineering vol.10 no.7 pp.743 – 746. (See the PDF file.) [Taylor color scheme ]

Thompson JD, Higgins DG and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680. [Clustal X color scheme ]

Thorne JL, Kishino H, Painter IS (December, 1998). “Estimating the rate of evolution of the rate of molecular evolution”. Mol. Biol. Evol. 15 (12): 1647–57. (See the PubMed entry the PubMed entry)

Troshin PV, Procter JB and Barton GJ (2011). “Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment – JABAWS:MSA.” Bioinformatics; doi: 10.1093/bioinformatics/btr304.

Waterhouse AM, Procter JB, Martin DMA, Clamp M and Barton GJ (2009). “JalView version 2: a multiple sequence alignment and analysis workbench.” Bioinformatics 25:1189 – 1191. (See on PMC.) [Discusses methodology later used to create the Taylor and Zappo color schemes ]

Welling GW, Weijer WJ, van der Zee R and Welling-Wester S (1985). “Prediction of sequential antigenic regions in proteins.” FEBS Letters, Vol. 188, No. 2: 215-218.

Yang ZR, Thomson R, McMeil P and Esnouf RM (2005). RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21: 3369-3376.