An information system on genomic elements and predicted protein structures of buffalo (Bubalus bubalis)
Among the livestock species, buffalo remained as an integral part of the Indian rural economy. With the advent of genome sequencing technologies, it became possible to sequence the whole genome of Murrah buffalo. Also, significant amount of information on different genomic elements of buffalo is av...
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| Format: | Article |
| Language: | English |
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Indian Council of Agricultural Research
2021-04-01
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| Series: | Indian Journal of Animal Sciences |
| Subjects: | |
| Online Access: | https://epubs.icar.org.in/index.php/IJAnS/article/view/111494 |
| _version_ | 1828005978452262912 |
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| author | AMIT KAIRI TANMAYA KUMAR SAHU ATMAKURI RAMAKRISHNA RAO |
| author_facet | AMIT KAIRI TANMAYA KUMAR SAHU ATMAKURI RAMAKRISHNA RAO |
| author_sort | AMIT KAIRI |
| collection | DOAJ |
| description |
Among the livestock species, buffalo remained as an integral part of the Indian rural economy. With the advent of genome sequencing technologies, it became possible to sequence the whole genome of Murrah buffalo. Also, significant amount of information on different genomic elements of buffalo is available at National Centre for Biotechnology Information (NCBI). However, the positions of these elements on the genome are not fully known. In addition, the 3D structures of buffalo proteins are not available and also there exist no browser to visualize important genic elements on buffalo genome. Hence, a study was taken up to develop a web-based information system having information on genomic elements, protein 3-D structures and genome browser. Initially, information on nucleotide and protein sequences were retrieved from NCBI and parsed suitably. Later, the protein structures were predicted, validated, refined and stabilized in silico. An Information System on Buffalo Genome (ISBG) with 3-tier architecture was developed containing the sequence and structural information. ISBG contains complete coding sequences (CDS), Mitochondrial DNAs, 1k upstream regions and Untranslated Regions (UTRs) of buffalo genome. The buffalo genes were also mapped onto the genome. The results revealed that maximum number of genes were found distributed on chromosome 4 followed by chromosome 18, which can also be visualized from the developed genome browser. ISBG can be accessed at http://cabgrid.res.in:8080/bgis. The proposed information system helps animal breeders and biotechnologist in animal improvement.
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| first_indexed | 2024-04-10T07:50:13Z |
| format | Article |
| id | doaj.art-bb14e1dba94a4e4bbed84191ca6fcad8 |
| institution | Directory Open Access Journal |
| issn | 0367-8318 2394-3327 |
| language | English |
| last_indexed | 2024-04-10T07:50:13Z |
| publishDate | 2021-04-01 |
| publisher | Indian Council of Agricultural Research |
| record_format | Article |
| series | Indian Journal of Animal Sciences |
| spelling | doaj.art-bb14e1dba94a4e4bbed84191ca6fcad82023-02-23T10:16:47ZengIndian Council of Agricultural ResearchIndian Journal of Animal Sciences0367-83182394-33272021-04-01901110.56093/ijans.v90i11.111494An information system on genomic elements and predicted protein structures of buffalo (Bubalus bubalis)AMIT KAIRI0TANMAYA KUMAR SAHU1ATMAKURI RAMAKRISHNA RAO2ICAR–Indian Agricultural Statistics Research Institute. New Delhi 110 012 IndiaICAR–Indian Agricultural Statistics Research Institute. New Delhi 110 012 IndiaICAR–Indian Agricultural Statistics Research Institute. New Delhi 110 012 India Among the livestock species, buffalo remained as an integral part of the Indian rural economy. With the advent of genome sequencing technologies, it became possible to sequence the whole genome of Murrah buffalo. Also, significant amount of information on different genomic elements of buffalo is available at National Centre for Biotechnology Information (NCBI). However, the positions of these elements on the genome are not fully known. In addition, the 3D structures of buffalo proteins are not available and also there exist no browser to visualize important genic elements on buffalo genome. Hence, a study was taken up to develop a web-based information system having information on genomic elements, protein 3-D structures and genome browser. Initially, information on nucleotide and protein sequences were retrieved from NCBI and parsed suitably. Later, the protein structures were predicted, validated, refined and stabilized in silico. An Information System on Buffalo Genome (ISBG) with 3-tier architecture was developed containing the sequence and structural information. ISBG contains complete coding sequences (CDS), Mitochondrial DNAs, 1k upstream regions and Untranslated Regions (UTRs) of buffalo genome. The buffalo genes were also mapped onto the genome. The results revealed that maximum number of genes were found distributed on chromosome 4 followed by chromosome 18, which can also be visualized from the developed genome browser. ISBG can be accessed at http://cabgrid.res.in:8080/bgis. The proposed information system helps animal breeders and biotechnologist in animal improvement. https://epubs.icar.org.in/index.php/IJAnS/article/view/111494Buffalo genomeGenome browserGenomic elementsInformation systemProtein StructureWeb-interface |
| spellingShingle | AMIT KAIRI TANMAYA KUMAR SAHU ATMAKURI RAMAKRISHNA RAO An information system on genomic elements and predicted protein structures of buffalo (Bubalus bubalis) Indian Journal of Animal Sciences Buffalo genome Genome browser Genomic elements Information system Protein Structure Web-interface |
| title | An information system on genomic elements and predicted protein structures of buffalo (Bubalus bubalis) |
| title_full | An information system on genomic elements and predicted protein structures of buffalo (Bubalus bubalis) |
| title_fullStr | An information system on genomic elements and predicted protein structures of buffalo (Bubalus bubalis) |
| title_full_unstemmed | An information system on genomic elements and predicted protein structures of buffalo (Bubalus bubalis) |
| title_short | An information system on genomic elements and predicted protein structures of buffalo (Bubalus bubalis) |
| title_sort | information system on genomic elements and predicted protein structures of buffalo bubalus bubalis |
| topic | Buffalo genome Genome browser Genomic elements Information system Protein Structure Web-interface |
| url | https://epubs.icar.org.in/index.php/IJAnS/article/view/111494 |
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