title: A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.
abstract: The standardization and sharing of data and tools are the biggest challenges of large collaborative projects such as the Encyclopedia of DNA Elements (ENCODE). Here we describe a compact Web application, Galaxy2(ENCODE), that effectively addresses these issues. It provides an intuitive interface for the deposition and access of data, and features a vast number of analysis tools including operations on genomic intervals, utilities for manipulation of multiple sequence alignments, and molecular evolution algorithms. By providing a direct link between data and analysis tools, Galaxy2(ENCODE) allows addressing biological questions that are beyond the reach of existing software. We use Galaxy2(ENCODE) to show that the ENCODE regions contain >2000 unannotated transcripts under strong purifying selection that are likely functional. We also show that the ENCODE regions are representative of the entire genome by estimating the rate of nucleotide substitution and comparing it to published data. Although each of these analyses is complex, none takes more than 15 min from beginning to end. Finally, we demonstrate how new tools can be added to Galaxy2(ENCODE) with almost no effort. Every section of the manuscript is supplemented with QuickTime screencasts. Galaxy2(ENCODE) and the screencasts can be accessed at http://g2.bx.psu.edu.
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Blankenberg
authors.forename: James
authors.initials: J
authors.lastname: Taylor
authors.forename: Ian
authors.initials: I
authors.lastname: Schenck
authors.forename: Jianbin
authors.initials: J
authors.lastname: He
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.forename: Matthew
authors.initials: M
authors.lastname: Ghent
authors.forename: Narayanan
authors.initials: N
authors.lastname: Veeraraghavan
authors.forename: Istvan
authors.initials: I
authors.lastname: Albert
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: Kateryna D
authors.initials: KD
authors.lastname: Makova
authors.forename: Ross C
authors.initials: RC
authors.lastname: Hardison
authors.forename: Anton
authors.initials: A
authors.lastname: Nekrutenko
mesh_terms: D030541:Databases, Genetic; D015894:Genome, Human; D006801:Humans; D020407:Internet; D017422:Sequence Analysis, DNA; D012984:Software