UCSC Genome Browser

https://genome.ucsc.edu

Methods

linear single view single scale single focus segregated partial abstraction no arrangement no interconnection segment sparse type segment contiguous type point sparse type point contiguous type

Tool

Access Format web application
Supported Files notapplicable
License unavailable
Tool name

UCSC Genome Browser
Tool Link https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A11102837-11267747&hgsid=729714349_6ib6LxPNBWK6CgShBpt2CkgFUcIX
Documentation https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html

Paper

The human genome browser at UCSC.

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12: 996–1006.

Abstract

As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.