Galaxy: a platform for interactive large-scale genome analysis

Abstract

Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.

Figure 1.

Galaxy supports several variations of the basic set operations, to accommodate the fact that our elements are coordinate-based regions rather than simple atomic objects.

Figure 2.

Galaxy history system for querying UCSC Table Browser. (A) UCSC Table Browser page sending results to Galaxy. (B) Galaxy's history page with a single query. (C) History page showing how Galaxy can be used to find intersection between two queries. (D) History page displaying intersection results.

Figure 3.

Examples of promoters characterized by binding of the transcription initiation complex and/or high conservation. Images from the UCSC Genome Browser generated via Galaxy illustrate (A) a promoter that has strong conservation (indicative of purifying selection) and biochemical evidence of binding by RNA polymerase II and TAF1, (B) a promoter that is poorly conserved but is strongly bound by RNA polymerase II and TAF1, and (C) a strongly conserved promoter that is not bound by the transcription initiation machinery in the cells tested. The track labeled “galaxy” is the custom track automatically generated by Galaxy for each query number (34, 35, and 36). Genes are labeled and have exons as boxes and introns as lines with arrowheads pointing in the direction of transcription. “Conservation” is the phastCons track followed by positions of aligning DNA in homologous regions of other species. The positions of promoters are shown as rectangles. The results of chromatin immunoprecipitations (ChIP data) are plotted as the negative log of the p-value, ranging in the vertical direction from 0 to 10.0 and with a continuous thin line placed at the threshold of 2.0. Positions of repeats identified by RepeatMasker (A.F.A. Smit and P. Green, unpubl., http://ftp.genome.washington.edu/RM/RepeatMasker.html) are shown as black rectangles in panels B and C.