Abstract
Multiple sequence alignment (MSA) is an essential approach to apply in other outstanding bioinformatics tasks such as structural predictions, biological function analyses or phylogenetic modeling. However, current MSA methodologies do not reach a consensus about how sequences must be accurately aligned. Moreover, these tools usually provide partially optimal alignments, as each one is focused on specific features. Thus, the same set of sequences can provide quite different alignments, overall when sequences are less related. Consequently, researchers and biologists do not agree on how the quality of MSAs should be evaluated in order to decide the most adequate methodology. Therefore, recent evaluations tend to use more complex scores including supplementary biological features. In this work, we address the evaluation of MSAs by using a novel supervised learning approach based on Least Square Support Vector Machine (LS-SVM). This algorithm will include a set of heterogeneous features and scores in order to determine the alignment accuracies. It is assessed by means of the benchmark BAliBASE.
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Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H.Z., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N., Yeh, L.S.L.: Uniprot: the universal protein knowledgebase. Nucleic Acids Res. 32, D115–D119 (2004)
Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalov, I., Bourne, P.: The protein data bank. Nucleic Acids Research 28(1), 235–242 (2000)
Bradley, R.K., Roberts, A., Smoot, M., Juvekar, S., Do, J., Dewey, C., Holmes, I., Pachter, L.: Fast Statistical Alignment. PLoS Computational Biology 5(5) (2009)
Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R., Apweiler, R.: The gene ontology annotation (goa) database: sharing knowledge in uniprot with gene ontology. Nucleic Acids Res. 32, D262–D266 (2004)
Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.: A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure 5(3), 345–352 (1979)
De Brabanter, K., Karsmakers, P., Ojeda, F., Alzate, C., De Brabanter, J., Pelckmans, K., De Moor, B., Vandewalle, J., Suykens, J.A.K.: Ls-svmlab: a matlab toolbox for least squares support vector machines, v1.8 (2011)
Do, C., Mahabhashyam, M., Brudno, M., Batzoglou, S.: ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Research 15(2), 330–340 (2005)
Edgar, R.: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5), 1792–1797 (2004)
Estévez, P.A., Tesmer, M., Perez, C.A., Zurada, J.M.: Normalized mutual information feature selection. IEEE Transactions on Neural Networks 20(2), 189–201 (2009)
Finn, R.D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J.E., Gavin, O.L., Gunasekaran, P., Ceric, G., Forslund, K., Holm, L., Sonnhammer, E.L.L., Eddy, S.R., Bateman, A.: The pfam protein families database. Nucleic Acids Res. 38, D211–D222 (2010)
Henikoff, S., Henikoff, J.G.: Amino-acid substitution matrices from protein blocks. In: Proceedings of the National Academy of Sciences of the United States of America, vol. 89(22), pp. 10915–10919 (1992)
Katoh, K., Misawa, K., Kuma, K., Miyata, T.: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30(14), 3059–3066 (2002)
Kemena, C., Notredame, C.: Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 25(19), 2455–2465 (2009)
Kemena, C., Taly, J.F., Kleinjung, J., Notredame, C.: Strike: evaluation of protein msas using a single 3d structure. Bioinformatics 27(24), 3385–3391 (2011)
Lassmann, T., Sonnhammer, E.: Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6 (2005)
Li, H., Homer, N.: A survey of sequence alignment algorithms for next-generation sequencing. Briefings in Bioinformatics 11(5), 473–483 (2010)
Lin, K., Kleinjung, J., Taylor, W.R., Heringa, J.: Testing homology with contact accepted mutation (cao): a contact-based markov model of protein evolution. Computational Biology and Chemistry 27(2), 93–102 (2003)
Notredame, C., Higgins, D., Heringa, J.: T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302(1), 205–217 (2000)
O’Sullivan, O., Suhre, K., Abergel, C., Higgins, D., Notredame, C.: 3DCoffee: Combining protein sequences and structures within multiple sequence alignments. Journal of Molecular Biology 340(2), 385–395 (2004)
Pei, J.: Multiple protein sequence alignment. Current Opinion in Structural Biology 18(3), 382–386 (2008)
Pei, J., Grishin, N.V.: PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics 23, 802–808 (2007)
Styczynski, M.P., Jensen, K.L., Rigoutsos, I., Stephanopoulos, G.: BLOSUM62 miscalculations improve search performance. Nature Biotechnology 26(3), 274–275 (2008)
Suykens, J.A.K., Van Gestel, T., De Brabanter, J., De Moor, B., Vandewalle, J.: Least Squares Support Vector Machines. World Scientific Pub. Co. Inc., Singapore (2003)
Szabo, A., Novak, A., Miklos, I., Hein, J.: Reticular alignment: A progressive corner-cutting method for multiple sequence alignment. BMC Bioinformatics 11 (2010)
Thompson, J., Higgins, D., Gibson, T.: ClustalW: Improving the sensivity of progressive multiple sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22(22), 4673–4680 (1994)
Thompson, J., Koehl, P., Ripp, R., Poch, O.: BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins-Structure Function and Bioinformatics 61(1), 127–136 (2005)
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Ortuño, F., Valenzuela, O., Pomares, H., Rojas, I. (2013). Evaluating Multiple Sequence Alignments Using a LS-SVM Approach with a Heterogeneous Set of Biological Features. In: Rojas, I., Joya, G., Cabestany, J. (eds) Advances in Computational Intelligence. IWANN 2013. Lecture Notes in Computer Science, vol 7903. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38682-4_18
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DOI: https://doi.org/10.1007/978-3-642-38682-4_18
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