vHoT: a database for predicting interspecies interactions between viral microRNA and host genomes
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Some viruses have been reported to transcribe microRNAs, implying complex relationships between the host and the pathogen at the post-transcriptional level through microRNAs in virus-infected cells. Although many computational algorithms have been developed for microRNA target prediction, few have been designed exclusively to find cellular or viral mRNA targets of viral microRNAs in a user-friendly manner. To address this, we introduce the viral microRNA host target (vHoT) database for predicting interspecies interactions between viral microRNA and host genomes. vHoT supports target prediction of 271 viral microRNAs from human, mouse, rat, rhesus monkey, cow, and virus genomes. vHoT is freely available at http://dna.korea.ac.kr/vhot.
KeywordsTarget Prediction Interspecies Interaction Viral miRNAs Predict miRNA Target Secondary Structure Prediction Algorithm
Funding: This work was supported by the National Research Foundation (NRF) funded by the Korean Government Ministry of Education, Science and Technology (MEST) [2011-0009963 to S.Y., 2011-0005462 to H.M.].
- 20.Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (2009) Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10:295PubMedCrossRefGoogle Scholar
- 28.Bessant C, Shadforth I, Oakley D (2009) Building bioinformatics solutions: with Perl, R and MySQL. Oxford biology. Oxford University Press, OxfordGoogle Scholar
- 29.Descartes A, Bunce T (2000) Programming the Perl DBI. O’Reilly, CambridgeGoogle Scholar
- 30.Zawodny JD, Balling DJ (2004) High performance MySQL: optimization, backups, replication, and load balancing, 1st edn. O’Reilly, BeijingGoogle Scholar