Multiple sequence alignment

Multiple sequence alignment based on combining genetic algorithm with chaotic sequences

C. Gao, Wang, B., Zhou, C. J., Zhang, Q., Gao, C., Wang, B., Zhou, C. J., and Zhang, Q., Multiple sequence alignment based on combining genetic algorithm with chaotic sequences, vol. 15, p. -, 2016.

In bioinformatics, sequence alignment is one of the most common problems. Multiple sequence alignment is an NP (nondeterministic polynomial time) problem, which requires further study and exploration. The chaos optimization algorithm is a type of chaos theory, and a procedure for combining the genetic algorithm (GA), which uses ergodicity, and inherent randomness of chaotic iteration. It is an efficient method to solve the basic premature phenomenon of the GA.

Genome-wide identification and expression profiling of the fatty acid desaturase gene family in the silkworm, Bombyx mori

Q. M. Chen, Cheng, D. J., Liu, S. P., Ma, Z. G., Tan, X., and Zhao, P., Genome-wide identification and expression profiling of the fatty acid desaturase gene family in the silkworm, Bombyx mori, vol. 13, pp. 3747-3760, 2014.

Fatty acid desaturases exist in all living organisms and play important roles in many different biologic processes, such as fatty acid metabolism, lipid biosynthetic processes, and pheromone biosynthetic processes. Using the available silkworm genome sequence, we identified 14 candidate fatty acid desaturase genes. Eleven genes contain 3 conserved histidine cluster motifs and 4 transmembrane domains, but their N-terminal residues exhibit obvious diversity.

Isolation and characterization of NBS-LRR- resistance gene candidates in turmeric (Curcuma longa cv. surama)

R. K. Joshi, Mohanty, S., Subudhi, E., and Nayak, S., Isolation and characterization of NBS-LRR- resistance gene candidates in turmeric (Curcuma longa cv. surama), vol. 9, pp. 1796-1806, 2010.

Turmeric (Curcuma longa), an important asexually reproducing spice crop of the family Zingiberaceae is highly susceptible to bacterial and fungal pathogens. The identification of resistance gene analogs holds great promise for development of resistant turmeric cultivars. Degenerate primers designed based on known resistance genes (R-genes) were used in combinations to elucidate resistance gene analogs from Curcuma longa cultivar surama. The three primers resulted in amplicons with expected sizes of 450-600 bp.

Building multiple sequence alignments with a flavor of HSSP alignments

R. Hiroshi Higa, da Cruz, S. Aparecido, Kuser, P. Regina, Yamagishi, M. Eduardo Be, Fileto, R., Oliveira, S. Robson de, Mazoni, I., Santos, E. Henrique d, Neshich, G., and Mancini, A. Luiz, Building multiple sequence alignments with a flavor of HSSP alignments, vol. 5, pp. 127-137, 2006.

Homology-derived secondary structure of proteins (HSSP) is a well-known database of multiple sequence alignments (MSAs) which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB. It is also used by STING and JavaProtein Dossier to calculate and present relative entropy as a measure of the degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB.

A simple genetic algorithm for multiple sequence alignment

C. Gondro and Kinghorn, B. P., A simple genetic algorithm for multiple sequence alignment, vol. 6, pp. 964-982, 2007.

Multiple sequence alignment plays an important role in molecular sequence analysis. An alignment is the arrangement of two (pairwise alignment) or more (multiple alignment) sequences of ‘residues’ (nucleotides or amino acids) that maximizes the similarities between them. Algorithmically, the problem consists of opening and extending gaps in the sequences to maximize an objective function (measurement of similarity). A simple genetic algorithm was developed and implemented in the software MSA-GA.

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