Aligning Multiple Protein Sequences by Hybrid Clonal Selection Algorithm with Insert-Remove-Gaps and BlockShuffling Operators

• Published in: Artificial Immune Systems pp. 321 - 334
• Main Authors: Cutello, V., Lee, D., Nicosia, G., Pavone, M., Prizzi, I.
• Format: Book Chapter Conference Proceeding
• Language: English
• Published: Berlin, Heidelberg Springer Berlin Heidelberg 2006; Springer
• Series: Lecture Notes in Computer Science
• Subjects: Applied sciences; Artificial intelligence; bioinformatics; clonal selection algorithms; Computer science; control theory; systems; Data processing. List processing. Character string processing; Exact sciences and technology; hypermutation operator; immune algorithms; Memory organisation. Data processing; multiple sequence alignment; protein sequences; Software; Program library; DNA; Sequence alignment; Objective function; Sequence analysis; Task analysis; Artificial intelligence; Optimization; Protein; Clone; Immune system
• ISBN: 3540377492; 9783540377498
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/11823940_25

Multiple sequence alignment (MSA) is one of the most important tasks in biological sequence analysis. This paper will primarily focus on on protein alignments, but most of the discussion and methodology also applies to DNA alignments. A novel hybrid clonal selection algorihm, called an aligner, is presented. It searches for a set of alignments amongst the population of candidate alignments by optimizing the classical weighted sum of pairs objective function. Benchmarks from BaliBASE library (v.1.0 and v.2.0) are used to validate the algorithm. Experimental results of BaliBASE v.1.0 benchmarks show that the proposed algorithm is superior to PRRP, ClustalX, SAGA, DIALIGN, PIMA, MULTIALIGN, and PILEUP8. On BaliBASE v.2.0 benchmarks the algorithm shows interesting results in terms of SP score with respect to established and leading methods, i.e. ClustalW, T-Coffee, MUSCLE, PRALINE, ProbCons, and Spem.