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Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB.

Lee JH, Lee T, Lee HK, Cho BW, Shin DH, Do KT, Sung S, Kwak W, Kim HJ, Kim H, Cho S, Park KD - Asian-australas. J. Anim. Sci. (2014)

Bottom Line: In order to better understand horses, more variants and other integrated information are needed.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.

View Article: PubMed Central - PubMed

Affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Horse SNP database web page. Horse single nucleotide polymorphism and expression database (HSDB) is available at http://snugenome2.snu.ac.kr/HSDB. (A) Users can search SNP or corresponding gene information using SNP position or RS ID or gene symbol. After searching the SNP, user can see the SNPs within the gene, there are several colors depending their effect. User will get more detail information including reference and alternative allele information, SNP position, SNP quality, depth, and effect impact (high, moderate, low, modifier) which definition follows snpEff. HSDB also enables the user to obtain gene annotation information including transcript ID and gene description, gene ontology term and orthology ID with human and mouse. Users can see the linkage disequilibrium map of interest gene. (B) Advanced Search provides similar results of SNP Search, but user can search the SNPs with many filtering options. (C) HSDB provides expression information of muscle and blood from 4 horses both before and after exercise, especially DEG information. User can search the expression information according to their interest using the Advanced Tools of Expression Search. SNP, single nucleotide polymorphism.
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f1-ajas-27-9-1236: Horse SNP database web page. Horse single nucleotide polymorphism and expression database (HSDB) is available at http://snugenome2.snu.ac.kr/HSDB. (A) Users can search SNP or corresponding gene information using SNP position or RS ID or gene symbol. After searching the SNP, user can see the SNPs within the gene, there are several colors depending their effect. User will get more detail information including reference and alternative allele information, SNP position, SNP quality, depth, and effect impact (high, moderate, low, modifier) which definition follows snpEff. HSDB also enables the user to obtain gene annotation information including transcript ID and gene description, gene ontology term and orthology ID with human and mouse. Users can see the linkage disequilibrium map of interest gene. (B) Advanced Search provides similar results of SNP Search, but user can search the SNPs with many filtering options. (C) HSDB provides expression information of muscle and blood from 4 horses both before and after exercise, especially DEG information. User can search the expression information according to their interest using the Advanced Tools of Expression Search. SNP, single nucleotide polymorphism.

Mentions: HSDB used comprehensive genomic information source from horse with human and mouse to confirm gene predictions that have been integrated with external data. HSDB is available at http://snugenome2.snu.ac.kr/HSDB. This database displays novel SNPs detected using RNA-seq as well as SNPs from re-sequencing data. Also this database displays an expression level and LD map for SNPs in the selected genes. The web interface allows interactive use of the information related to the horse variants. The interface consists of five menus: Introduction, SNP Search, Advanced Search, Expression Search, and Contact (Figure 1). Users can obtain variant information from the SNP Search and Advanced Search menu, and expression information from the Expression Search menu. Genetic variants and expression information can be searched by gene symbol or SNP position and the query will retrieve an array of results including a distribution of variants, gene information, expression and differentially expressed test results.


Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB.

Lee JH, Lee T, Lee HK, Cho BW, Shin DH, Do KT, Sung S, Kwak W, Kim HJ, Kim H, Cho S, Park KD - Asian-australas. J. Anim. Sci. (2014)

Horse SNP database web page. Horse single nucleotide polymorphism and expression database (HSDB) is available at http://snugenome2.snu.ac.kr/HSDB. (A) Users can search SNP or corresponding gene information using SNP position or RS ID or gene symbol. After searching the SNP, user can see the SNPs within the gene, there are several colors depending their effect. User will get more detail information including reference and alternative allele information, SNP position, SNP quality, depth, and effect impact (high, moderate, low, modifier) which definition follows snpEff. HSDB also enables the user to obtain gene annotation information including transcript ID and gene description, gene ontology term and orthology ID with human and mouse. Users can see the linkage disequilibrium map of interest gene. (B) Advanced Search provides similar results of SNP Search, but user can search the SNPs with many filtering options. (C) HSDB provides expression information of muscle and blood from 4 horses both before and after exercise, especially DEG information. User can search the expression information according to their interest using the Advanced Tools of Expression Search. SNP, single nucleotide polymorphism.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150188&req=5

f1-ajas-27-9-1236: Horse SNP database web page. Horse single nucleotide polymorphism and expression database (HSDB) is available at http://snugenome2.snu.ac.kr/HSDB. (A) Users can search SNP or corresponding gene information using SNP position or RS ID or gene symbol. After searching the SNP, user can see the SNPs within the gene, there are several colors depending their effect. User will get more detail information including reference and alternative allele information, SNP position, SNP quality, depth, and effect impact (high, moderate, low, modifier) which definition follows snpEff. HSDB also enables the user to obtain gene annotation information including transcript ID and gene description, gene ontology term and orthology ID with human and mouse. Users can see the linkage disequilibrium map of interest gene. (B) Advanced Search provides similar results of SNP Search, but user can search the SNPs with many filtering options. (C) HSDB provides expression information of muscle and blood from 4 horses both before and after exercise, especially DEG information. User can search the expression information according to their interest using the Advanced Tools of Expression Search. SNP, single nucleotide polymorphism.
Mentions: HSDB used comprehensive genomic information source from horse with human and mouse to confirm gene predictions that have been integrated with external data. HSDB is available at http://snugenome2.snu.ac.kr/HSDB. This database displays novel SNPs detected using RNA-seq as well as SNPs from re-sequencing data. Also this database displays an expression level and LD map for SNPs in the selected genes. The web interface allows interactive use of the information related to the horse variants. The interface consists of five menus: Introduction, SNP Search, Advanced Search, Expression Search, and Contact (Figure 1). Users can obtain variant information from the SNP Search and Advanced Search menu, and expression information from the Expression Search menu. Genetic variants and expression information can be searched by gene symbol or SNP position and the query will retrieve an array of results including a distribution of variants, gene information, expression and differentially expressed test results.

Bottom Line: In order to better understand horses, more variants and other integrated information are needed.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.

View Article: PubMed Central - PubMed

Affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus