A Bioinformatics Platform for Electricigens Analysis

来源 :第五届全国生物信息学与系统生物学学术大会 | 被引量 : 0次 | 上传用户:newnew111
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  Background: As renewable energy, microbial fuel cells (MFCs) are gaining increasing concern and have been developed well for its peculiar advantages.Up to now, however, the efficiency of MFCs is too low to be used in application for large scale.Among all of the factors that influence the performance of MFCs, electricigens, a kind of microbes which conserve energy to support growth by oxidizing organic compounds to carbon dioxide with direct quantitative electron transfer to electrodes, play a key role, and their mechanism of current generating is very important for researches of MFCs.Here we collected and classified the data and resources related to electricigens to construct a database and an analytical platform for them.Our work will help researchers to find genes related to electron generating and transferring, realize the mechanism of current generating for a specific microbe, and then manipulate the microbe with approaches of genetic engineering.Methods: A database named EGBase (Electricigens Genomes dataBase) was established, in which the microbes were collected from biomedical literatures both manually and automatically.The database was designed and constructed according to the electricigens data from different resources such as E-Utilities, NCBI RefSeq and Google Scholar.Then we provided a tool named RPGM (Re-annotating Protein-coding Genes in Microbial genomes), which was based on an algorithm for detecting the over-annotated protein-coding genes in microorganisms by integrating TN curve and Z curve.Finally, we constructed an online analytical platform.This platform integrates with some analytical tools, which include RPGM, GBrowse and BLAST, as well as providing basic functions for EGBase, such as data browsing, data searching and so on.Results: Up to now, the EGBase provides annotations for 477,144 genes from 222 genomes that include 10 Geobacter genomes and 34 Shewanella genomes.85 of these genomes were conformed as electricigens manually, while the others were collected automatically.The platform website (http://www.cbi.seu.edu.cn/electricigens) contains all the data from EGBase and provides several analytical tools.Conclusions: The EGBase and its analytical platform were designed to provide not only highly integrative information for electricigens genomes, but also useful analytical tools for users.The platform website can be accessed free and will help users in MFCs researches .
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