Abstract
Revolutionary DNA sequencing technology has enabled affordable genome sequencing for numerous species. Thousands of species already have completely decoded genomes, and tens of thousands more are in progress. Naturally, parallel expansion of the functional parts list library is anticipated, yet genome-level understanding of function also requires maps of functional relationships, such as functional protein networks. Such networks have been constructed for many sequenced species including common model organisms. Nevertheless, the majority of species with sequenced genomes still have no protein network models available. Moreover, biologists might want to obtain protein networks for their species of interest on completion of the genome projects. Therefore, there is high demand for accessible means to automatically construct genome-scale protein networks based on sequence information from genome projects only. Here, we present a public web server, JiffyNet, specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a query species with only protein sequences provided. Assessment of the networks by JiffyNet demonstrated generally high predictive ability for pathway annotations. Furthermore, JiffyNet provides network visualization and analysis pages for wide variety of molecular concepts to facilitate network-guided hypothesis generation. JiffyNet is freely accessible at http://www.jiffynet.org.
Highlights
With advanced DNA sequencing and genome assembly technology, >4000 completely decoded genomes have already been deposited in public databases as reported by Genome Online Database of January 2013
The same database reported 15 000 more genome projects in progress; tens of thousands of completely sequenced species will be publicly available in the few years
We compared the quality of the orthology-based networks by JiffyNet and BIPS, another public web server capable of constructing orthology-based protein networks [10], using identical query protein sequence input data
Summary
With advanced DNA sequencing and genome assembly technology, >4000 completely decoded genomes have already been deposited in public databases as reported by Genome Online Database (http://www.genomesonline.org) of January 2013. For further functional interrogation of the query species protein network, JiffyNet provides subnetwork visualization and analysis pages for wide variety of molecular concepts [7] by Gene Ontology (GO) [8] and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway [9] definitions. JiffyNet first maps orthologous relationships between all input query proteins and all proteins of the selected template species using the INPARANOID algorithm (http://inparanoid.sbc.su.se) [16].
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