Vir-Mir db: prediction of viral microRNA candidate hairpins.
MicroRNAs have been found in various organisms and play essential roles in gene expression regulation of many critical cellular processes. Large-scale computational prediction of miRNAs has been conducted for many organisms using known genomic sequences; however, there has been no such effort for the thousands of known viral genomes. Some viruses utilize existing host cellular pathways for their own benefit. Furthermore, viruses are capable of encoding miRNAs and using them to repress host genes. Thus, identifying potential miRNAs in all viral genomes would be valuable to virologists who study virus-host interactions. Based on our previously reported hairpin secondary structure and feature selection filters, we have examined the 2266 available viral genome sequences for putative miRNA hairpins and identified 33 691 hairpin candidates in 1491 genomes. Evaluation of the system performance indicated that our discovery pipeline exhibited 84.4% sensitivity. We established an interface for users to query the predicted viral miRNA hairpins based on taxonomic classification, and a host target gene prediction service based on the RNAhybrid program and the 3'-UTR gene sequences of human, mouse, rat, zebrafish, rice and Arabidopsis. The viral miRNA prediction database (Vir-Mir) can be accessed via http://alk.ibms.sinica.edu.tw.
Li
Sung-Chou
SC
Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan, Republic of China.
Shiau
Cheng-Kai
CK
Lin
Wen-Chang
WC
D020413:3' Untranslated Regions / Q000737:chemistry; D000818:Animals; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D016679:Genome, Viral; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry* / Q000145:classification; D016366:Open Reading Frames; D012367:RNA, Viral / Q000737:chemistry* / Q000145:classification; D051381:Rats; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface
D020413:3' Untranslated Regions; D035683:MicroRNAs; D012367:RNA, Viral
Dev Biol. 1999 Dec 15;216(2):671-80
10642801
Nucleic Acids Res. 2007 Jan;35(Database issue):D381-5
17148483
Mol Cell. 2003 May;11(5):1253-63
12769849
Genome Biol. 2003;4(7):R42
12844358
Dev Cell. 2003 Aug;5(2):337-50
12919683
Cell. 2004 Jan 23;116(2):281-97
14744438
Science. 2004 Mar 26;303(5666):2022-5
12893888
Science. 2004 Apr 30;304(5671):734-6
15118162
RNA. 2004 Oct;10(10):1507-17
15383676
Mol Cell. 2004 Dec 22;16(6):861-5
15610730
Cell. 2005 Jan 14;120(1):21-4
15652478
Cell. 2005 Mar 11;120(5):635-47
15766527
Nat Genet. 2005 May;37(5):495-500
15806104
Retrovirology. 2004;1:43
15601472
Development. 2005 Nov;132(21):4645-52
16224044
BMC Bioinformatics. 2005;6:267
16274478
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D135-9
16381831
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4
16381832
RNA. 2006 Feb;12(2):192-7
16373484
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W451-4
16845047
BMC Genomics. 2006;7:164
16813663
Nucleic Acids Res. 2007 Jan;35(Database issue):D149-55
17108354
Genes Dev. 2002 Jul 1;16(13):1616-26
12101121