Blast Implementation (Study of Performance)

1.Abstract

Recently, in bioinformatic area of study, many scientists and researchers admit the need of information technology in their field. This is because the previous research records closed up to approximately 97 billion based sequence and over 93 million records. Scientist begin to accumulate DNA and protein sequence data at an exponential rate. In 1991, US National Center for Biotechnology Information created a system called BLAST that stands for Basic Local Alignment Searching Tool. This machine functions as a database that stores many data recorded from the research by the biology scientist. BLAST able to make annotation and comparisons much easier.

2.Keywords
BLAST +
3.Objective

There are some objectives in our researches. First, by running BLAST program into different input it can evaluate the performance of HPC (High Performance Computing) in LIPI. Second, by using BLAST this can be a method to obtain the profile of HPC in LIPI. Third, it is to enable the researcher to compare a query sequence with a library or databases of sequences. Forth, through BLAST it enable to find high scoring ungapped segments among related sequences. Fifth, the objective is to find out how to install the BLAST program into the company computer system and connect it with server. Lastly, the objective is how to compile the coding BLAST by using C language.

4.Methodology

For our experiment of BLAST, there will be a certain method that we will use to obtain a certain result. First, we will do experiment with variety sizes wether in database or in query. Second, we are going to select different kind of algorithm that designed for specific research. Third method is setting different computational profile; for example by adjusting number of processor cores. Lastly is using GPU if the BLAST support the GPU system.

5.Team

Dr. Rifki Sadikin
Dr. Esa Prakasa
Nuramira Shafinaz Zulailee
Nor Alana Rosli

6.Computation plan (required processor core hours, data storage, software, etc)

- BLAST program installer
- Server

7.Source of funding
-
8.Target/outputs
7 August 2018
9.Date of usage
09/07/2018 - 07/08/2018
10.Gpu usage
use gpu
11.Supporting files
prop_1531103303.pdf
12.Created at
09/07/2018
13.Approval status
approved