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Vir-Mir db: prediction of viral microRNA candidate hairpins.

Li SC, Shiau CK, Lin WC - Nucleic Acids Res. (2007)

Bottom Line: MicroRNAs have been found in various organisms and play essential roles in gene expression regulation of many critical cellular processes.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan, Republic of China.

ABSTRACT
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.

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Target gene search web interface. Presently, we provide the 3′-UTR region sequences of human, mouse, rat, zebrafish, rice and Arabidopsis for target gene prediction. The RNAhybrid program is applied for the target search (19,20). Users can directly submit the predicted viral miRNA hairpin sequences from the viral miRNA web interface or submit their own miRNA sequences for target gene prediction. We have a helix constraint option to let users select different seed match region to be used in the target prediction pipeline. Since it is difficult to correctly predict the mature miRNA from the hairpin structure. It is suggested this target prediction information should be used for preliminary exploration purpose.
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Figure 4: Target gene search web interface. Presently, we provide the 3′-UTR region sequences of human, mouse, rat, zebrafish, rice and Arabidopsis for target gene prediction. The RNAhybrid program is applied for the target search (19,20). Users can directly submit the predicted viral miRNA hairpin sequences from the viral miRNA web interface or submit their own miRNA sequences for target gene prediction. We have a helix constraint option to let users select different seed match region to be used in the target prediction pipeline. Since it is difficult to correctly predict the mature miRNA from the hairpin structure. It is suggested this target prediction information should be used for preliminary exploration purpose.

Mentions: It is of researchers’ interest to learn about viral miRNAs and their host target genes. To assist biologists, we provide an integrated interface to identify possible host target genes of the viral miRNA in selected host genomes using the RNAhybrid program (19,20). Presently, as shown in Figure 4, we provided the 3′-UTR region sequences of reference genes from human, mouse, rat, zebrafish, rice and Arabidopsis as the search target dataset. We retrieved 3′ UTRs based on the coding sequence positions acquired individually from the human.rna.gbff file (from NCBI on 19 December 2005), mouse.rna.gbff file (from NCBI on 19 December 2005), rat.rna.gbff file (from NCBI on 19 December 2005), zebrafish.rna.gbff file (from NCBI on 19 June 2006) and plant1 ∼ 5.rna.gbff file (from NCBI on 5 August 2006).Figure 4.


Vir-Mir db: prediction of viral microRNA candidate hairpins.

Li SC, Shiau CK, Lin WC - Nucleic Acids Res. (2007)

Target gene search web interface. Presently, we provide the 3′-UTR region sequences of human, mouse, rat, zebrafish, rice and Arabidopsis for target gene prediction. The RNAhybrid program is applied for the target search (19,20). Users can directly submit the predicted viral miRNA hairpin sequences from the viral miRNA web interface or submit their own miRNA sequences for target gene prediction. We have a helix constraint option to let users select different seed match region to be used in the target prediction pipeline. Since it is difficult to correctly predict the mature miRNA from the hairpin structure. It is suggested this target prediction information should be used for preliminary exploration purpose.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238904&req=5

Figure 4: Target gene search web interface. Presently, we provide the 3′-UTR region sequences of human, mouse, rat, zebrafish, rice and Arabidopsis for target gene prediction. The RNAhybrid program is applied for the target search (19,20). Users can directly submit the predicted viral miRNA hairpin sequences from the viral miRNA web interface or submit their own miRNA sequences for target gene prediction. We have a helix constraint option to let users select different seed match region to be used in the target prediction pipeline. Since it is difficult to correctly predict the mature miRNA from the hairpin structure. It is suggested this target prediction information should be used for preliminary exploration purpose.
Mentions: It is of researchers’ interest to learn about viral miRNAs and their host target genes. To assist biologists, we provide an integrated interface to identify possible host target genes of the viral miRNA in selected host genomes using the RNAhybrid program (19,20). Presently, as shown in Figure 4, we provided the 3′-UTR region sequences of reference genes from human, mouse, rat, zebrafish, rice and Arabidopsis as the search target dataset. We retrieved 3′ UTRs based on the coding sequence positions acquired individually from the human.rna.gbff file (from NCBI on 19 December 2005), mouse.rna.gbff file (from NCBI on 19 December 2005), rat.rna.gbff file (from NCBI on 19 December 2005), zebrafish.rna.gbff file (from NCBI on 19 June 2006) and plant1 ∼ 5.rna.gbff file (from NCBI on 5 August 2006).Figure 4.

Bottom Line: MicroRNAs have been found in various organisms and play essential roles in gene expression regulation of many critical cellular processes.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan, Republic of China.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus