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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: 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.

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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Related in: MedlinePlus

Expanded view of taxonomy table. The classification and arrangement of viral miRNA candidate hairpins are based on the taxonomy table of NCBI. The numbers in the right parentheses of each classification level indicate the numbers of candidate hairpins found in those levels. By clicking on a link, users can see the expanded table. The numbers in parentheses indicate the number of candidate hairpins found in that particular viral genome.
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Figure 2: Expanded view of taxonomy table. The classification and arrangement of viral miRNA candidate hairpins are based on the taxonomy table of NCBI. The numbers in the right parentheses of each classification level indicate the numbers of candidate hairpins found in those levels. By clicking on a link, users can see the expanded table. The numbers in parentheses indicate the number of candidate hairpins found in that particular viral genome.

Mentions: Due to the large number of prediction results, we constructed a user-friendly web interface to present the viral candidate miRNAs. As shown in Figures 1 and 2, the classification and arrangement of the viral candidates are according to the taxonomy table of NCBI, so users can query the viral miRNAs more easily. Users may query the putative miRNAs from a specific virus by using the hierarchical menu or by using the simple search function. A keyword search can be performed, but users are recommended to use it with the GenBank identifier or RefSeq accession number for better search result, e.g. 30844336 or NC_003663 for Cowpox virus.Figure 1.


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

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

Expanded view of taxonomy table. The classification and arrangement of viral miRNA candidate hairpins are based on the taxonomy table of NCBI. The numbers in the right parentheses of each classification level indicate the numbers of candidate hairpins found in those levels. By clicking on a link, users can see the expanded table. The numbers in parentheses indicate the number of candidate hairpins found in that particular viral genome.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Expanded view of taxonomy table. The classification and arrangement of viral miRNA candidate hairpins are based on the taxonomy table of NCBI. The numbers in the right parentheses of each classification level indicate the numbers of candidate hairpins found in those levels. By clicking on a link, users can see the expanded table. The numbers in parentheses indicate the number of candidate hairpins found in that particular viral genome.
Mentions: Due to the large number of prediction results, we constructed a user-friendly web interface to present the viral candidate miRNAs. As shown in Figures 1 and 2, the classification and arrangement of the viral candidates are according to the taxonomy table of NCBI, so users can query the viral miRNAs more easily. Users may query the putative miRNAs from a specific virus by using the hierarchical menu or by using the simple search function. A keyword search can be performed, but users are recommended to use it with the GenBank identifier or RefSeq accession number for better search result, e.g. 30844336 or NC_003663 for Cowpox virus.Figure 1.

Bottom Line: 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.

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