Skip to main content

Table 2 Feature comparison of the UCSC Genome Browser, Ensembl Genome Browser and NCBI MapViewer.

From: Comparison of human (and other) genome browsers

  UCSC Ensembl NCBI
Presentation Genome in horizontal orientation Main page contains a single graphic displaying annotation ('tracks')
Clicking on annotation element presents web page of detailed information and links to other resources
Genome in horizontal orientation Main ContigView page contains three graphics displaying annotations at different resolutions
Clicking on annotation element presents box with links to other resources or Views with more detailed information
Genome in vertical orientation Annotations graphically presented in columns ('maps')
Clicking on annotation elements or links in columns provides quick access to other, primarily NCBI, resources
Content 13 vertebrate, 15 invertebrate Many cross-species annotations including conservation across eight species ENCODE Project annotations 13 vertebrate, six invertebrate Heavy focus on gene annotations such as Ensembl genes and VEGA HapMap project-related Views 11 vertebrate, five invertebrate, one protozoan, 12 plant, eight fungi Annotations primarily from NCBI resources
Functionality Text search, BLAT sequence search, isPCR primer search
Advanced annotation extraction using Table Browser Ability to upload and view own annotations
Text search, BLAST and SSAHA sequence search, e-PCR primer search
Advanced annotation extraction using BioMart Ability to upload and view own annotations Simultaneous view of syntenic regions
Text search, BLAST sequence search, e-PCR primer search
Basic annotation extraction
  1. Abbreviations: BLAT, BLAST-like alignment tool; ENCODE, ENCyclopedia Of DNA Elements; e-PCR, electronic polymerase chain reaction; NCBI, National Center for Biotechnology Information; SSAHA, Sequence search and alignment by hashing algorithm; UCSC, University of California Santa Cruz; VEGA, Vertebrate Genome Annotation.