Molecular Biotechnology

, Volume 38, Issue 3, pp 269–275

The Genome Browser at UCSC for Locating Genes, and Much More!

Review

DOI: 10.1007/s12033-007-9019-2

Cite this article as:
Bina, M. Mol Biotechnol (2008) 38: 269. doi:10.1007/s12033-007-9019-2

Abstract

For beginners in the field, this review highlights the key features of the genome browser at UCSC for data display, and provides nearly step-by-step procedures for creating publication quality maps. The browser offers an engine (Blat) for searching a known genomic DNA for correspondence with protein and DNA sequences specified by the user. The results provide links to graphical displays, known as maps. Users can create “designer maps” by adding Tracks to view various types of data and specific landmarks. The browser offers an extensive list of options. They include the position of annotated genes, the position of reference cDNA sequences (RefSeq from GenBank), the position of alternatively spliced mRNA species, and predictions derived from computational models to identify potential transcription start sites and potential protein binding elements in genomic DNA. Several tracks can be tailored for comparative genomics. The browser also offers tracks for displaying large-scale experimental data including gene expression profiles, exon chips, and single-nucleotide-polymorphisms.

Keywords

The Human Genome ProjectGenome browsersGene mappingGene displayLandmarks in genomic DNA

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  1. 1.Department of ChemistryPurdue UniversityWest LafayetteUSA