STUDY AND IMPLEMENTATION OF SST AND SMITH-WATERMAN ALGORITHM USING PERL.

• Main Author: Christinawati Buulolo(NIM : 13505604), Inte
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/8244
• Institution: Institut Teknologi Bandung

Abstract: <br /> <br /> <br /> <br /> <br /> <br /> molecular is growing fast. That is why data genetics were become huge every year. Analyzing to data genetics manually is not efficient, so people use algorithms and <br /> <br /> <br /> <br /> <br /> <br /> computer technology. One kind activity to analyze data genetics is sequence alignment. The purpose of sequence alignment is to find sequence similarity between two or more than two gen. <br /> <br /> <br /> <br /> <br /> <br /> There were many algorithms to find sequence similarity. Some of them are Smith-Waterman (SW), BLAST, and Sequence Search Tree (SST) algorithm. SW is the most accurate algorithm to find sequence similarity and that is why this algorithm is called gold standard. BLAST is the most popular algorithm because this algorithm is faster than <br /> <br /> <br /> <br /> <br /> <br /> SW. So BLAST is used as reference to others new algorithms. SST, the newest algorithm than BLAST and SW, is faster than BLAST but less accurate than BLAST. <br /> <br /> <br /> <br /> <br /> <br /> In this final project, a software module namely SST&SW Module had been build to find sequence similarity from DNA sequence accurately in the sort time. This module <br /> <br /> <br /> <br /> <br /> <br /> implements a method namely SST&SW method which is created from combination of SST and SW algorithm. An SST&SW Module is run on Linux or Unix platform and has been build from Perl. <br /> <br /> <br /> <br /> <br /> <br /> SST&SW Module had been tested on some cases and its result had been compared with BLAST and SW algorithm. The result show that the complexity and time performance of <br /> <br /> <br /> <br /> <br /> <br /> SST&SW Module is smaller than SW, but is bigger than BLAST. Nevertheless, SST&SW Module is more accurate than BLAST.