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Genome Browsers were developed in response to the problem of visualizing genome assemblies and associated data. In this section, you will learn about their history and how to start using the UCSC Genome Browser to search for a gene.
Accessing the Browser and Tools
The UCSC Genome Bioinformatics website consists of a suite of tools for the viewing and mining of genomic data.
To visualize this gene in the UCSC Genome Browser in the context of various genomic annotations, the user must follow a series of important steps.
A large volume of biological data is displayed in genomic context. In this section, you will learn how to start examining these annotations to learn more about a gene.
Learn about the default views that the UCSC Genome Browser displays for annotation tracks as well as other user-controlled display modes.
Each annotation track has an associated description page that details the methods and data sources used to produce the track, validation, credits, and citations of relevant publications.
A selection of commonly used data tracks are explored. In this section, you will learn how to find out more about a gene of interest.
Phenotype and Disease Associations Tracks
Learn how to use data from large-scale sequencing projects that have found genetic associations with observable phenotypic traits and the presence of medical conditions.
Gene and Gene Prediction Tracks
Learn about the various tracks available through the UCSC Genome Browser.
GenBank mRNA and EST Sequence Alignments
The mRNA and EST tracks show sequences from GenBank that align well to the genome using BLAT.
Genomes can be aligned to each other in order to study their evolution, to find homologs, and to determine the location of potentially functional genomic regions. In this section, you will learn about functional elements predicted from conservation data as well as experimentally-defined regulatory elements. You will also learn how to order a clone for use in biological experiments to further study a gene of interest.
Conservation and Regulation Data
Learn about this track that shows a 44-species multiple alignment of vertebrate genomes created using the MULTIZ alignment program and histograms of conservation scores associated with the alignment.
Learn how the user can order a cDNA clone of this gene for experimental research that avoids the time-consuming process of cloning cDNA.
In this section, there are frequently asked questions and a summary of the tutorial. Additionally, you will learn how to find further documentation and help on using the UCSC Bioinformatics website.
