Identifying the definite base of COI for extraction of DNA sequences using LPBS

Author

Abdullah, Sharifah Lailee Syed ; Harun, Hazaruddin ; Hussin, Naimah Mohd ; Hamid, Jiwa Noris ; Hanaphi, Roziana Mohamed

Author_Institution

Fac. of Comput. Sci. & Math., UiTM Arau, Arau, Malaysia

fYear

2012

fDate

24-27 June 2012

Firstpage

1145

Lastpage

1148

Abstract

This paper presents the use of the `Linear-PSO with Binary Search´ (LPBS) algorithm for discovering motifs, especially species-specific motifs. In this study, two samples from different fragments of `mitochondrial cytochrome C oxidase subunit I´ (COI/COX1) were collected from the Genbank online database. DNA sequences for the first sample are a mix of different fragments of COI and the second sample is from the same fragment of COI. The genome of COI was used as a reference set and other DNA sequences were used as a comparison set. All the collected DNA sequences are from the same species. The results show that the LPBS algorithm is able to discover motifs of greater length when using DNA sequences from the same fragment of COI. The experiment also found that 139 can be used as a starting base for COI DNA sequences extraction to discover species-specific motifs.

Keywords

DNA; biology computing; enzymes; genomics; molecular biophysics; particle swarm optimisation; DNA sequences; Genbank online database; genome; linear-PSO-with-binary search algorithm; mitochondrial cytochrome C oxidase subunit I; particle swarm optimization; species-specific motifs; Algorithm design and analysis; Animals; Bioinformatics; DNA; Databases; Genomics; Particle swarm optimization; Linear-PSO; Particle Swarm Optimization; motif discovery; species specific;

fLanguage

English

Publisher

ieee

Conference_Titel

Humanities, Science and Engineering Research (SHUSER), 2012 IEEE Symposium on

Conference_Location

Kuala Lumpur

Print_ISBN

978-1-4673-1311-7

Type

conf

DOI

10.1109/SHUSER.2012.6268794

Filename

6268794