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A comparative account of microRNA resources, feature-validations and application-based categorizations : SPECIES: virus
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
vHoT
http://dna.korea.ac.kr/vhot.
vHoT database predicts interspecies interactions between viral microRNA and host genomes.
Kim H, Park S, Min H, Yoon S.vHoT: a database for predicting interspecies interactions between viral microRNA and host genomes.Arch Virol. 2012 Mar;157(3):497-501. doi: 10.1007/s00705-011-1181-y.PMID: 22160653
2012
50
miRBase
http://www.mirbase.org/
A major microRNA repository comprising of microRNA sequences and annotation obtained from published literature wherein both precursor and mature sequences can be retrieved from the database.
Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7. Epub 2010 Oct 30. PubMed PMID: 21037258 Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8. Epub 2007 Nov 8. PubMed PMID: 17991681
2011
66
Bi-targeting
http://www.cs.bgu.ac.il/~vaksler/BiTargeting.htm
In silico tool designed to identify viral and human microRNAs that function together in regulating host gene expression.
Veksler-Lublinsky I, Shemer-Avni Y, Kedem K, Ziv-Ukelson M. Gene bi-targeting by viral and human miRNAs. BMC Bioinformatics. 2010 May 13;11:249. PubMed PMID: 20465802.
2010
100
To be validated
miRNEST
http://mirnest.amu.edu.pl
Comprehensive database on animal, plant and virus microRNA including details on species that are of importance in medical and agricultural research.
Szczesniak MW, Deorowicz S, Gapski J, Kaczynski L, Makalowska I. miRNEST database: an integrative approach in microRNA search and annotation. Nucleic Acids Res. 2012 Jan;40(Database issue):D198-204. Epub 2011 Dec 1. PubMed PMID: 22135287; PubMed Central PMCID: PMC3245016.
2012
100
RepTar
http://reptar.ekmd.huji.ac.il
Database on genome-wide computed details of human and mouse microRNAs as well as of cellular targets of human and mouse viral microRNAs.
Elefant N, Berger A, Shein H, Hofree M, Margalit H, Altuvia Y. RepTar: a database of predicted cellular targets of host and viral miRNAs. Nucleic Acids Res. 2011 Jan;39(Database issue):D188-94. Epub 2010 Dec 10. PubMed PMID: 21149264
2010
100
Dataset downloadable
Vir-Mir-db
http://alk.ibms.sinica.edu.tw
Web based resource that allows a user to explore predicted viral microRNA hairpins and their corresponding host target gene.
Li SC, Shiau CK, Lin WC. Vir-Mir db: prediction of viral microRNA candidate hairpins. Nucleic Acids Res. 2008 Jan;36(Database issue):D184-9. Epub 2007 Aug 15. PubMed PMID: 17702763
2008
100
ViTa
http://vita.mbc.nctu.edu.tw/
Online resource comprising of virus data retrieved from databases such as miRBase, ICTV, VirGen, VBRC, and miRNAMap. Provides access to several tools to study microRNA and virus interaction.
Hsu PW, Lin LZ, Hsu SD, Hsu JB, Huang HD. ViTa: prediction of host microRNAs targets on viruses. Nucleic Acids Res. 2007 Jan;35(Database issue):D381-5. Epub 2006 Dec 5. PubMed PMID: 17148483
2007
100
VMir
URL not found
Computational tool to identify potential precursor microRNAs in viral genome.
Grundhoff A, Sullivan CS, Ganem D. A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses. RNA. 2006 May;12(5):733-50. Epub 2006 Mar 15. PubMed PMID: 16540699; PubMed Central PMCID: PMC1440911.
2006
100
Source code available from the authors upon request
 
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