Abstract
Quantitative comparison of sequences can be performed pairwise by aligning two sequences based on considerations of gaps representing insertions or deletions and matches between nucleotides and amino acids. Pairwise comparisons can be performed as global alignments if it is known that the sequences are homologous in their full length or by local alignments if it is known that one sequence is shorter than the other. The dynamic programming algorithms for constructing global and local alignments will be described in detail and relevant computer programs suggested. The different strategies behind multiple alignments are described including relevant computer programs. The search program BLAST is introduced in detail and different applications described.
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References
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403–410.
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402.
Durbin, R., Eddy, S., Krogh, A. and Mitchison, G. 1999. Biological sequence analysis. Cambridge Univ. Press.
Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792–1797
Feng, D. F. & Dolittle, R. F. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, 351–60.
Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999;41:95–98.
Higgins, D. G. & Sharp, P. M. 1988. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237–244.
Karlin, S., & Altschul, S. F. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci USA 87, 2264–8.
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., Higgins, D. G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948.
Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S., Jobb, G., Förster, W., Brettske, I., Gerber, S., Ginhart, A. W., Gross, O., Grumann, S., Hermann, S., Jost, R., König, A., Liss, T., Lüssmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., Schleifer, K. H. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371.
Moreno-Hagelsieb, G. & Latimer, K. 2008. Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 24:319–24.
Needleman, S. B. & Wunsch, C. D. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453.
Nei, M. & Kumar, S. 2000. Molecular evolution and phylogenetics. Oxford University Press.
Notredame, C., Higgins, D.G., Heringa, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302: 205–217.
Rice, P., Longden, I., & Bleasby, A. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genetics 16:276–277.
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D. & Higgins, D. G. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using ClustalOmega. Mol. Syst. Biol. 7:539.
Smith, T. F., Waterman, M. S. & Fitch, W. M. 1981 Comparative biosequence metrics. J. Mol. Evol. 18, 38–46.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28: 2731–2739.
Thompson, J. D., Plewniak, F. & Poch, O. 1999. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 15:87–88.
Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M., Barton, G. J. 2009. Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191.
Yamada, K.D., Tomii, K., Katoh, K. 2016. Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees. Bioinformatics32, 3246–3251.
Zuker, M. & Jacobson, A. B. 1998. Using Reliability Information to Annotate RNA Secondary Structures. RNA 4, 669–679, 1998.
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Christensen, H., Olsen, J.E. (2018). Pairwise Alignment, Multiple Alignment, and BLAST. In: Christensen, H. (eds) Introduction to Bioinformatics in Microbiology. Learning Materials in Biosciences. Springer, Cham. https://doi.org/10.1007/978-3-319-99280-8_4
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