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Comparative Study
. 2007 Jun;17(6):960-4.
doi: 10.1101/gr.5578007.

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly

Daniel Blankenberg  1 , James Taylor, Ian Schenck, Jianbin He, Yi Zhang, Matthew Ghent, Narayanan Veeraraghavan, Istvan Albert, Webb Miller, Kateryna D Makova, Ross C Hardison, Anton Nekrutenko
Affiliations
Comparative Study

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly

Daniel Blankenberg et al. Genome Res. 2007 Jun.

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.

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Figures

Figure 1.
Figure 1.
Galaxy2ENCODE supports several variations of the basic set operations designed specifically for manipulation of genomic intervals.
Figure 2.
Figure 2.
Types of Non-GENCODE ESTs.
Figure 3.
Figure 3.
Steps (A–G) in identification of Non-GENCODE ESTs. Galaxy2 makes such analyses transparent. See Methods and Screencast 15 for explanations of each step.
See this image and copyright information in PMC

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