Identifying the definite base of COI for extraction of DNA sequences using LPBS
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 on...
| Main Authors: | , , , , |
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| Format: | Conference or Workshop Item |
| Language: | English |
| Published: |
2012
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| Online Access: | https://repo.uum.edu.my/id/eprint/20639/1/SHSER%202012%201145%201148.pdf |
| _version_ | 1825804407569121280 |
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| author | Syed Abdullah, Sharifah Lailee Harun, Hazaruddin Mohd Hussin, Naimah Hamid, Jiwa Noris Mohamed Hanaphi, Roziana |
| author_facet | Syed Abdullah, Sharifah Lailee Harun, Hazaruddin Mohd Hussin, Naimah Hamid, Jiwa Noris Mohamed Hanaphi, Roziana |
| author_sort | Syed Abdullah, Sharifah Lailee |
| collection | UUM |
| description | 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. |
| first_indexed | 2024-07-04T06:14:02Z |
| format | Conference or Workshop Item |
| id | uum-20639 |
| institution | Universiti Utara Malaysia |
| language | English |
| last_indexed | 2024-07-04T06:14:02Z |
| publishDate | 2012 |
| record_format | eprints |
| spelling | uum-206392017-01-18T03:18:11Z https://repo.uum.edu.my/id/eprint/20639/ Identifying the definite base of COI for extraction of DNA sequences using LPBS Syed Abdullah, Sharifah Lailee Harun, Hazaruddin Mohd Hussin, Naimah Hamid, Jiwa Noris Mohamed Hanaphi, Roziana QA75 Electronic computers. Computer science 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. 2012-06-24 Conference or Workshop Item PeerReviewed application/pdf en https://repo.uum.edu.my/id/eprint/20639/1/SHSER%202012%201145%201148.pdf Syed Abdullah, Sharifah Lailee and Harun, Hazaruddin and Mohd Hussin, Naimah and Hamid, Jiwa Noris and Mohamed Hanaphi, Roziana (2012) Identifying the definite base of COI for extraction of DNA sequences using LPBS. In: 2012 IEEE Symposium on Humanities, Science and Engineering Research (SHUSER), 24-27 June 2012, Kuala Lumpur. http://doi.org/10.1109/SHUSER.2012.6268794 doi:10.1109/SHUSER.2012.6268794 doi:10.1109/SHUSER.2012.6268794 |
| spellingShingle | QA75 Electronic computers. Computer science Syed Abdullah, Sharifah Lailee Harun, Hazaruddin Mohd Hussin, Naimah Hamid, Jiwa Noris Mohamed Hanaphi, Roziana Identifying the definite base of COI for extraction of DNA sequences using LPBS |
| title | Identifying the definite base of COI for extraction of DNA sequences using LPBS |
| title_full | Identifying the definite base of COI for extraction of DNA sequences using LPBS |
| title_fullStr | Identifying the definite base of COI for extraction of DNA sequences using LPBS |
| title_full_unstemmed | Identifying the definite base of COI for extraction of DNA sequences using LPBS |
| title_short | Identifying the definite base of COI for extraction of DNA sequences using LPBS |
| title_sort | identifying the definite base of coi for extraction of dna sequences using lpbs |
| topic | QA75 Electronic computers. Computer science |
| url | https://repo.uum.edu.my/id/eprint/20639/1/SHSER%202012%201145%201148.pdf |
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