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 s

SUBMITTER: Blankenberg D 

PROVIDER: S-EPMC1891355 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature