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Bioinformatics Software: UCSC Genome Browser

UCSC Genome Browser

The UCSC Genome Browser provides flexible access to genomic sequences and aligned annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more) for over 40 model organisms.  It can also be used for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets.

Main Features

  • Genome Browser: visualize genomic sequence and annotation tracks
  • Table Browser: text-based access to the database underlying the Genome Browser
  • Custom Tracks: upload user data to the Genome Browser and overlay user data with existing/custom annotation tracks
  • BLAT: a fast sequence alignment tool similar to BLAST
  • Gene Sorter: retrieve genes with similar features (e.g. expression profiles, homology, protein family, etc.)
  • In-Silico PCR: quick search of the genome with PCR primer pairs. 
  • Liftover: converts genome coordinates and genome annotation files between assemblies
  • Proteome: protein information search hub
  • Human ENCODE projects: fully searchable ENCODE data and display at UCSC genome browser
  • Many other features