Quick2D

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View alignment of viral DNA ligases. Paste example alignment.
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Prediction Methods

PSIPRED
D. T. Jones (1999) Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292, 195-202.
 
JNET
J. A. Cuff and G. J. Barton (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40, 502-511.
 
Prof
M. Ouali and R. D. King (2000) Cascaded multiple classifiers for secondary structure prediction. Protein Science 9, 1162-1176.
 
Prof
B. Rost (2001) Protein secondarystructure prediction continues to rise. Journal of Structural Biology 134, 204-218.
 
Coils
A. N. Lupas, M. Van Dyke and J. Stock (1991) Predicting Coiled Coils from Protein Sequences. Science 252, 1162-1164.
 
HMMTOP
G. E. Tusnády and I. Simon (1998) Principles Governing Amino Acid Composition of Integral Membrane Proteins: Applications to Topology Prediction. Journal of Molecular Biology 283, 489-506.
 
MEMSAT-SVM
Timothy Nugent, David T. Jones (2009) Transmembrane protein topology prediction using support vector machines BMC Bioinformatics 2009
 
PHOBIUS
Lukas Käll, Anders Krogh and Erik L. L. Sonnhammer. A Combined Transmembrane Topology and Signal Peptide Prediction Method. Journal of Molecular Biology 338(5):1027-1036, May 2004.
 
PREDISI
PrediSi: prediction of signal peptides and their cleavage positions. Hiller K, Grote A, Scheer M, M√ľnch R, Jahn D. Nucleic Acids Res 1;32, W375-9,Jul 2004.
 
DISOPRED2
J. J. Ward, J. S. Sodhi, L. J. McGuffin, B. F. Buxton and D. T. Jones (2004) Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life. Journal of Molecular Biology 337(3), 635-45.
 
IUPRED
Zsuzsanna Dosztá, Veronika Csizmók, Péter Tompa and István Simon (2005) The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins J. Mol. Biol. 347, 827-839.
 

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