| URL: | http://snugenome2.snu.ac.kr/HSDB |
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| Description: | HSDB is a database for providing gene centered SNPs and expression from NGS data of thoroughbred horse population. It helps to understand biology of horse by providing the expression and undetected SNP. HSDB consists of two parts: SNPs and expression. HSDB provide expression result, twenty-four sets of transcriptome data was generated for muscle and blood from six horses both before and after exercise. HSDB has successfully identified 3,418K of SNPs in horse genes include 5kb upstream and 5kb downstream region. The results display SNP types including, exon, intron, coding untranslated (UTR) regions, synonymous coding and non-synonymous coding. Identified variants were many by including rare variants of NGS as well as accurate. The identified SNPs were confirmed by comparing with SNP chip , the concordance were 99.02%. |
| Year founded: | 2014 |
| Last update: | 2014 |
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| Accessibility: |
Unaccessible
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| Country/Region: | Korea, Republic of |
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| University/Institution: | Seoul National University |
| Address: | Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea. |
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| Country/Region: | Korea, Republic of |
| Contact name (PI/Team): | Seoae Cho |
| Contact email (PI/Helpdesk): | moc.scimonegknc@eaoes |
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Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB. [PMID: 25178365]
Genetics is important for breeding and selection of horses but there is a lack of well-established horse-related browsers or databases. In order to better understand horses, more variants and other integrated information are needed. Thus, we construct a horse genomic variants database including expression and other information. Horse Single Nucleotide Polymorphism and Expression Database (HSDB) (http://snugenome2.snu.ac.kr/HSDB) provides the number of unexplored genomic variants still remaining to be identified in the horse genome including rare variants by using population genome sequences of eighteen horses and RNA-seq of four horses. The identified single nucleotide polymorphisms (SNPs) were confirmed by comparing them with SNP chip data and variants of RNA-seq, which showed a concordance level of 99.02% and 96.6%, respectively. Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants. The database will contribute to genetic improvement and breeding strategies of Thoroughbreds. |