Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold
Next generation sequencing technologies has revolutionized genomic research by producing a large volume of sequence data and lowest per base cost compared to the traditional sanger method. Although this technology offers many advantages, gap occurrences are commonly found in draft assemblies. The sa...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Science Publications
2015
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| Online Access: | http://psasir.upm.edu.my/id/eprint/16503/ http://psasir.upm.edu.my/id/eprint/16503/1/ajavsp.2015.133.140.pdf |
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| author | Balakrishnan, Krishnan Nair Abdullah, Ashwaq Ahmed Abba, Yusuf Bala, Jamilu Abubakar Abdullah, Faez Firdaus Jesse Mustaffa Kamal, Farina Allaudin, Zeenathul Nazariah Ideris, Aini Mohamed Mustapha, Noordin Mohd Lila, Mohd Azmi |
| author_facet | Balakrishnan, Krishnan Nair Abdullah, Ashwaq Ahmed Abba, Yusuf Bala, Jamilu Abubakar Abdullah, Faez Firdaus Jesse Mustaffa Kamal, Farina Allaudin, Zeenathul Nazariah Ideris, Aini Mohamed Mustapha, Noordin Mohd Lila, Mohd Azmi |
| author_sort | Balakrishnan, Krishnan Nair |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Next generation sequencing technologies has revolutionized genomic research by producing a large volume of sequence data and lowest per base cost compared to the traditional sanger method. Although this technology offers many advantages, gap occurrences are commonly found in draft assemblies. The same problem was observed with RatCytomegalovirus (RCMV) ALL-03 (Malaysia strain), where a complete genome sequence could not produce the complete genome due to the presence of gaps in the draft genome. This restrains our ability to take full advantage of genome data. This study aimed to identify the sequence data present in the gap regions and close these gaps in order to produce a complete genome sequence for RCMV ALL-03. Twenty sets of specific primers were designed between two adjacent contigs and PCR was carried out to obtain the appropriate sequences in respective gap regions. Sanger sequencing was employed in the PCR product to get the gap sequences. Out of the five identified gaps in the RCMV ALL-03 genome sequence, only three were confirmed to be true gaps, while the other two were due to sequence repeats. In conclusion, all the gaps were closed successfully and complete genome sequence of RCMV ALL-03 can now be explored in further studies. |
| first_indexed | 2025-11-15T08:07:45Z |
| format | Article |
| id | upm-16503 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T08:07:45Z |
| publishDate | 2015 |
| publisher | Science Publications |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-165032016-04-08T01:34:30Z http://psasir.upm.edu.my/id/eprint/16503/ Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold Balakrishnan, Krishnan Nair Abdullah, Ashwaq Ahmed Abba, Yusuf Bala, Jamilu Abubakar Abdullah, Faez Firdaus Jesse Mustaffa Kamal, Farina Allaudin, Zeenathul Nazariah Ideris, Aini Mohamed Mustapha, Noordin Mohd Lila, Mohd Azmi Next generation sequencing technologies has revolutionized genomic research by producing a large volume of sequence data and lowest per base cost compared to the traditional sanger method. Although this technology offers many advantages, gap occurrences are commonly found in draft assemblies. The same problem was observed with RatCytomegalovirus (RCMV) ALL-03 (Malaysia strain), where a complete genome sequence could not produce the complete genome due to the presence of gaps in the draft genome. This restrains our ability to take full advantage of genome data. This study aimed to identify the sequence data present in the gap regions and close these gaps in order to produce a complete genome sequence for RCMV ALL-03. Twenty sets of specific primers were designed between two adjacent contigs and PCR was carried out to obtain the appropriate sequences in respective gap regions. Sanger sequencing was employed in the PCR product to get the gap sequences. Out of the five identified gaps in the RCMV ALL-03 genome sequence, only three were confirmed to be true gaps, while the other two were due to sequence repeats. In conclusion, all the gaps were closed successfully and complete genome sequence of RCMV ALL-03 can now be explored in further studies. Science Publications 2015 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/16503/1/ajavsp.2015.133.140.pdf Balakrishnan, Krishnan Nair and Abdullah, Ashwaq Ahmed and Abba, Yusuf and Bala, Jamilu Abubakar and Abdullah, Faez Firdaus Jesse and Mustaffa Kamal, Farina and Allaudin, Zeenathul Nazariah and Ideris, Aini and Mohamed Mustapha, Noordin and Mohd Lila, Mohd Azmi (2015) Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold. American Journal of Animal and Veterinary Sciences, 10 (3). pp. 133-140. ISSN 1557-4555; ESSN: 1557-4563 http://thescipub.com/abstract/10.3844/ajavsp.2015.133.140 10.3844/ajavsp.2015.133.140 |
| spellingShingle | Balakrishnan, Krishnan Nair Abdullah, Ashwaq Ahmed Abba, Yusuf Bala, Jamilu Abubakar Abdullah, Faez Firdaus Jesse Mustaffa Kamal, Farina Allaudin, Zeenathul Nazariah Ideris, Aini Mohamed Mustapha, Noordin Mohd Lila, Mohd Azmi Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold |
| title | Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold |
| title_full | Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold |
| title_fullStr | Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold |
| title_full_unstemmed | Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold |
| title_short | Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold |
| title_sort | closing the gaps in rat cytomegalovirus all-03 (malaysian strain) genomic scaffold |
| url | http://psasir.upm.edu.my/id/eprint/16503/ http://psasir.upm.edu.my/id/eprint/16503/ http://psasir.upm.edu.my/id/eprint/16503/ http://psasir.upm.edu.my/id/eprint/16503/1/ajavsp.2015.133.140.pdf |