Protein sequencing alignment

Barton G J1996. Protein Sequence Alignment and Database Scanning. In Sternberg M E (Editor) Prote Structure Prediction - A Practical Approach. Oxford, IRL Press, pp. 31-63. 

GJ Barton. Protein sequence alignment and database scanning. In MJE Sternberg, ed. Protein Structure Prediction A Practical Approach. Oxford, UK IRE Press at Oxford Univ Press, 1998. 

WR Taylor. Multiple protein sequence alignment Algorithms and gap insertion. Methods Enzymol 266 343-367, 1996. 

P Briffeuil, G Baudoux, C Lambert, X De Bolle, C Vmals, E Feytmans, E Depiereux. Comparative analysis of seven multiple protein sequence alignment servers Clues to enhance reliability of predictions. Biomformatics 14 357-366, 1998. 

B Rost. Twilight zone of protein sequence alignments. Protein Eng 12 85-94, 1999. 

Gotoh, O. (1996). Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. /. Mol. Biol. 264, 823-838. 

Livingstone, C. D., and Barton, G.J. (1993). Protein sequence alignments a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci. 9, 745—756. 

M. Vingron and P. Argos. Determination of reliable regions in protein sequence alignments. Protein Eng, 5 565-569 (1990). 

Waterman, M. S. Jones, R. (1990). Consensus methods for DNA and protein sequence alignment. Methods Enzymol 183,221-37. 

J. M. Sauder, J. W. Arthur, R. L. Dunbrack, Jr. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins. 2000, 40, 6-22. 

We exemplify HMMs with Figure 1, which is taken from (Eddy, 1998). Figure 1 depicts a Markov model for protein sequence alignment. Sometimes this specific topology of a hidden Markov model is called a profile hidden Markov model There is a specific start state b and a specific final state e. The Match states (ml to m3) represent sequence positions. The Insert... 

To obtain a pairwise local alignment between the target sequence and A18R, click the Local button. The protein sequence alignment and accompanying statistics are then displayed in the bottom panel. 

Morgenstern, B., Dress, A. W. M., and Werner, T. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. USA 93, 12,098-12,103. 

Morgenstern, B. (2004) DIALIGN Multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res. 32, W33-W36. 

Protein sequence alignment has become an essential part of biomedical research. It is one of the standard approaches to explore potential functional activity of a newly discovered protein by identifying sequence homologues that may be evolutionarily related (1-3). One can often infer the structural and functional information of a new protein from the knowledge of well-characterized homologous proteins (4-7). In general, closely related protein sequences are... 

Wang, J. and Feng, J. A. (2005) NdPASA a novel pair-wise protein sequence alignment that incorporates neighbor-dependent amino acid propensities. Proteins 58, 628-637. 

Hannenhalli, S. S., and R. B. Russell. 2000. Analysis and prediction of functional sub-types from protein sequence alignments. J Mol Biol 303 61-76. 

R. Rechid, M. Vingron, and P. Argos. A new interactive protein sequence alignment program and comparison of its results with widely used algorithms. Comput. Applic. Biosci. 5 107-113 (1989). 

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