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.

Pattern-based Search of Epigenomic Data Using GeNemo

“…Pattern-based search tools for epigenomic data are essential for exploring the relationship between different epigenomic marks, which may lead to new biological insights. GeNemo, which searches by the content of the data and not metadata, is the first service of its kind to compare patterns in epigenomic data from published depositories such as the ENCODE database with a user-generated or downloaded dataset 5 . This marks the beginning of the availability of an epigenomic search tool that is widely accessible to researchers around the world just as text-based sequence search tool became widely available in the 1990s.…”

“…Since the first publication 5 of GeNemo as a web-based epigenomic data search tool, the Results section of GeNemo has been updated to have a matching appearance with GeNemo's front page. The old Results section closely mirrored the UCSC genome browser results section, and was largely dependent on the remote UCSC server for display.…”

“…Conventional text-based search engines are ineffective in this regard because, unlike DNA sequence, epigenomic data predominantly exist in the format of intensities or functional genomic regions. GeNemo, standing for Gene Nemo (as in Finding Nemo), was developed to address this unmet need using pattern-based searches 5 . Its algorithm utilizes a Markov Chain Monte Carlo maximization process 5 .…”

“…GeNemo, standing for Gene Nemo (as in Finding Nemo), was developed to address this unmet need using pattern-based searches 5 . Its algorithm utilizes a Markov Chain Monte Carlo maximization process 5 . Users take their own data or a dataset downloaded from depositories and search an array of online epigenomic data to identify similarities in patterns.…”

Omicseq: a web-based search engine for exploring omics datasets

“…The search engine is perhaps the most useful tool to explore the internet. We believe a search engine ( 17 ) is also critically important for exploring the massive collection of omics datasets. For the internet search engine, the key lies in its ability to accurately rank websites in terms of their relevancy to the query term.…”