The UCSC Table Browser data retrieval tool

The UCSC Table Browser data retrieval tool

2004 | Donna Karolchik*, Angela S. Hinrichs, Terrence S. Furey, Krishna M. Roskin, Charles W. Sugnet, David Haussler and W. James Kent
The UCSC Table Browser is a data retrieval tool that provides text-based access to genome assemblies and annotation data stored in the Genome Browser Database. It serves as a flexible alternative to the graphical-based Genome Browser, offering enhanced query support, including field value restrictions, free-form SQL queries, and combined queries on multiple tables. The tool allows users to filter and organize output into various formats, such as tab-delimited files or advanced formats for custom annotation tracks. The Table Browser User's Guide provides instructions and examples for constructing queries and configuring output. The tool is built on top of the Genome Browser Database, which consists of MySQL relational databases storing sequence and annotation data for various genome assemblies. Positional tables contain data associated with specific genome locations, while non-positional tables contain data not tied to genomic positions. The databases are optimized for interactive performance, with smaller tables indexed and larger tables split by chromosome. The UCSC Table Browser allows users to retrieve subsets of data from selected genome assemblies, filter results, and generate custom annotation tracks. It supports basic and advanced queries, including filtering, intersecting query results, and configuring output formats. The tool also provides output in various formats, such as GTF, BED, and FASTA, which can be used for further analysis or imported into other programs. The Table Browser is a powerful and flexible tool for querying and manipulating annotation tables within the Genome Browser Database. It allows users to extract subsets of data, generate custom annotation tracks, and perform complex queries. The tool is widely used by researchers for analyzing genomic data and is continually being improved to meet the needs of users.The UCSC Table Browser is a data retrieval tool that provides text-based access to genome assemblies and annotation data stored in the Genome Browser Database. It serves as a flexible alternative to the graphical-based Genome Browser, offering enhanced query support, including field value restrictions, free-form SQL queries, and combined queries on multiple tables. The tool allows users to filter and organize output into various formats, such as tab-delimited files or advanced formats for custom annotation tracks. The Table Browser User's Guide provides instructions and examples for constructing queries and configuring output. The tool is built on top of the Genome Browser Database, which consists of MySQL relational databases storing sequence and annotation data for various genome assemblies. Positional tables contain data associated with specific genome locations, while non-positional tables contain data not tied to genomic positions. The databases are optimized for interactive performance, with smaller tables indexed and larger tables split by chromosome. The UCSC Table Browser allows users to retrieve subsets of data from selected genome assemblies, filter results, and generate custom annotation tracks. It supports basic and advanced queries, including filtering, intersecting query results, and configuring output formats. The tool also provides output in various formats, such as GTF, BED, and FASTA, which can be used for further analysis or imported into other programs. The Table Browser is a powerful and flexible tool for querying and manipulating annotation tables within the Genome Browser Database. It allows users to extract subsets of data, generate custom annotation tracks, and perform complex queries. The tool is widely used by researchers for analyzing genomic data and is continually being improved to meet the needs of users.
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Understanding The UCSC Table Browser data retrieval tool