Identification of Viral Taxon-Specific Genes (VTSG): Application to
Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonom...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2018-12-01
|
| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e23.pdf |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832572220796305408 |
|---|---|
| author | Shinduck Kang Young-Chang Kim |
| author_facet | Shinduck Kang Young-Chang Kim |
| author_sort | Shinduck Kang |
| collection | DOAJ |
| description | Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma “protein structure determines its function,” we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks. |
| format | Article |
| id | doaj-art-9e5f4eff36f64e3da03b713d071a5e29 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-9e5f4eff36f64e3da03b713d071a5e292025-02-02T11:17:01ZengBioMed CentralGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e23524Identification of Viral Taxon-Specific Genes (VTSG): Application toShinduck KangYoung-Chang KimVirus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma “protein structure determines its function,” we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.http://genominfo.org/upload/pdf/gi-2018-16-4-e23.pdf coding regionconserved domain databasepairwise alignment sequence comparison RPS-BLAST |
| spellingShingle | Shinduck Kang Young-Chang Kim Identification of Viral Taxon-Specific Genes (VTSG): Application to Genomics & Informatics coding region conserved domain database pairwise alignment sequence comparison RPS-BLAST |
| title | Identification of Viral Taxon-Specific Genes (VTSG): Application to |
| title_full | Identification of Viral Taxon-Specific Genes (VTSG): Application to |
| title_fullStr | Identification of Viral Taxon-Specific Genes (VTSG): Application to |
| title_full_unstemmed | Identification of Viral Taxon-Specific Genes (VTSG): Application to |
| title_short | Identification of Viral Taxon-Specific Genes (VTSG): Application to |
| title_sort | identification of viral taxon specific genes vtsg application to |
| topic | coding region conserved domain database pairwise alignment sequence comparison RPS-BLAST |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e23.pdf |
| work_keys_str_mv | AT shinduckkang identificationofviraltaxonspecificgenesvtsgapplicationto AT youngchangkim identificationofviraltaxonspecificgenesvtsgapplicationto |