Multiple sequence alignment (MSA) is one of the topics of bio informatics that has seriously been researched. It is known as NP-complete problem. It is also considered as one of the most important and daunting tasks in computational biology. Concerning this a wide number of heuristic algorithms have been proposed to find optimal alignment. Among these heuristic algorithms are genetic algorithms (GA). The GA has mainly two major weaknesses: it is time consuming and can cause local minima. One of the significant aspects in the GA process in MSA is to maximize the similarities between sequences by adding and shuffling the gaps of Solution Coding (SC). Several ways for SC have been introduced. One of them is the Permutation Coding (PC). We propose a hybrid algorithm based on genetic algorithms (GAs) with a PC and 2-opt algorithm. The PC helps to code the MSA solution which maximizes the gain of resources, reliability and diversity of GA. The use of the PC opens the area by applying all functions over permutations for MSA. Thus, we suggest an algorithm to calculate the scoring function for multiple alignments based on PC, which is used as fitness function. The time complexity of the GA is reduced by using this algorithm. Our GA is implemented with different selections strategies and different crossovers. The probability of crossover and mutation is set as one strategy. Relevant patents have been probed in the topic.
Klebsiella pneumoniae producing extended-spectrum β-lactamase (ESBL) cause severe life threatening infections resulting in considerable morbidity and mortality especially in neonatology ward. The aim of this study was to evaluate the epidemiology and resistance of 131 strains collected between 2007 and 2008 in neonatology and pediatric wards and to determine the mode of their epidemic spread. The isolates were identified, tested for antimicrobial susceptibility with the disk-diffusion on Mueller-Hinton agar. The type of ESBL was determined by polymerase chain reaction (PCR) followed by sequencing for CTX-M enzymes. The epidemiological relationships between epidemic strains were analysed by pulsedfield gel electrophoresis. In this study, antibiotic susceptibility testing showed resistance to all β-lactams except imipenem with a concomitant resistance to aminoglycosides, tetracycline and cotrimoxazole. Fluoroquinolones still have activity against strains. Characterization of β-lactamases encoding genes revealed that all strains have SHV β-lactamases. TEM-type and CTX-M-1 group were encoded, respectively, in 21 and 57% of ESBLs isolates. Among 84 strains tested by PFGE, 14 pulsotypes were identified. DNA sequencing of amplified CTX-M β-lactamase genes justified diffusion of CTX-M-15 between epidemic strains. In conclusion, this study revealed a high degree of clonal diversity of isolates and complexity of outbreaks that involve more than two epidemic pulsotypes and indicated that both clonal spread of epidemic strains and transfer of β-lactamases might contribute to epidemic dissemination of ESBL in neonatology ward.
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