A COMPARISON OF IMPLEMENTATION EFFICIENCY OF NEEDLEMAN-WUNSCH AND SMITH-WATERMAN ALGORITHMS FOR SEQUENCE ALIGNMENT IN BIOINFORMATICS

Raziskovana in primerjana je učinkovitost implementacij algoritmov Needleman-Wunscha in Smith-Watermana za primerjave zaporedij na področju bioinformatike. Na podlagi implementacij smo nad enakimi podatki merili čase izvajanja v programskima jezikoma C++, Perl in statističnem jeziku R. Metodologija raziskovanja: Teoretična podlaga magistrske naloge temelji na ustreznih objavah različnih avtorjev in spletnih virov. Rezultati: Pri času izvajanja algoritmov v programskem jeziku C++ krajši vhodni niz ne presega 1 ms in daljši vhodni niz ne presega 15 ms. Pri programskem jeziku Perl in statičnem jeziku R, kjer se čas izvajanja z dolžino niza eksponentno povečuje. Sklep: Čas izvajanja algoritmov Needleman-Wunscha in Smith-Watermana z enakimi vhodnimi podatki v programskem jeziku C++, je krajši kot v programskem jeziku Perl ali statističnem jeziku R.In master\u27s thesis we were investigating and compared the effectiveness of the implementation of algorihms Needleman-Wunsch and Smith-Waterman for the comparison of sequences in the fields of bioinformatics. Based on the implementations of the same input data, we measured the time of execution in the programming language C++, Perl and statistical language R. Research methodology: Theoretical basis of the master\u27s thesis is based on relevant publications by various authors and online resources. Results: Execution time of algorithms in C++ programming language, the shorter input data does not exceed 1ms and long input data does not exceed 15ms. In programming language Perl or statistical language R, where the execution time with input data length increases exponentially. Conclusion: Execution time of algorithms Needleman-Wunsch and Smith-Watermn on the same input data in C++ programming language is shorter than in Perl or statistical language R