Paper Info
Title
GeNemo: a search engine for web-based functional genomic data.
Abstract
A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org.
Year
DOI
Venue
2016
10.1093/nar/gkw299
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
Bigwig,ENCODE,Information retrieval,Biology,Genomics,Data type,Datasets as Topic,Web application,Bioinformatics,Genetics,Big data,Pattern matching
Journal
44
Issue
ISSN
Citations 
W1
0305-1048
2
PageRank 
References 
Authors
0.38
0
3
Name
Order
Citations
PageRank
Yongqing Zhang143.79
Xiaoyi Cao2113.16
Sheng Zhong3215.39