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Cold Spring Harb Protoc. 2015 Dec 2;2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922.

The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations.

Author information

1
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120.

Abstract

Genomic-scale assays result in data that provide information over the entire genome. Such base pair resolution data cannot be summarized easily except via a graphical viewer. A genome browser is a tool that displays genomic data and experimental results as horizontal tracks. Genome browsers allow searches for a chromosomal coordinate or a feature, such as a gene name, but they do not allow searches by function or upstream binding site. Entry into a genome browser requires that you identify the gene name or chromosomal coordinates for a region of interest. A track provides a representation for genomic results and is displayed as a row of data shown as line segments to indicate regions of the chromosome with a feature. Another type of track presents a graph or wiggle plot that indicates the processed signal intensity computed for a particular experiment or set of experiments. Wiggle plots are typical for genomic assays such as the various next-generation sequencing methods (e.g., chromatin immunoprecipitation [ChIP]-seq or RNA-seq), where it represents a peak of DNA binding, histone modification, or the mapping of an RNA sequence. Here we explore the browser that has been built into the Saccharomyces Genome Database (SGD).

PMID:
26631126
PMCID:
PMC5673602
DOI:
10.1101/pdb.prot088922
[Indexed for MEDLINE]
Free PMC Article

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