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Viral IRES prediction system - a web server for prediction of the IRES secondary structure in silico.

Hong JJ, Wu TY, Chang TY, Chen CY - PLoS ONE (2013)

Bottom Line: IRES elements have been applied as useful tools for bi-cistronic expression vectors.Current RNA structure prediction programs are unable to predict precisely the potential IRES element.This advance useful search approach for IRES structures will facilitate IRES related studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan.

ABSTRACT
The internal ribosomal entry site (IRES) functions as cap-independent translation initiation sites in eukaryotic cells. IRES elements have been applied as useful tools for bi-cistronic expression vectors. Current RNA structure prediction programs are unable to predict precisely the potential IRES element. We have designed a viral IRES prediction system (VIPS) to perform the IRES secondary structure prediction. In order to obtain better results for the IRES prediction, the VIPS can evaluate and predict for all four different groups of IRESs with a higher accuracy. RNA secondary structure prediction, comparison, and pseudoknot prediction programs were implemented to form the three-stage procedure for the VIPS. The backbone of VIPS includes: the RNAL fold program, aimed to predict local RNA secondary structures by minimum free energy method; the RNA Align program, intended to compare predicted structures; and pknotsRG program, used to calculate the pseudoknot structure. VIPS was evaluated by using UTR database, IRES database and Virus database, and the accuracy rate of VIPS was assessed as 98.53%, 90.80%, 82.36% and 80.41% for IRES groups 1, 2, 3, and 4, respectively. This advance useful search approach for IRES structures will facilitate IRES related studies. The VIPS on-line website service is available at http://140.135.61.250/vips/.

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The distribution of R and pseudoknot parameters from positive and negative group of four IRES groups by VIPS analysis.The distribution of four IRES groups calculated by R and pseudoknot parameters in positive group and negative group. The R scores and pseudoknot scores were demonstrated according to IRES group 1 (a and e), IRES group 2 (b and f), IRES group 3 (c and g) and IRES group 4 (d and h). Linear discriminant analysis was applied to determine the cut-off line of the R score in each group shown as (a), (b), (c) and (d). Distribution of positive and negative IRES elements that were calculated and summarized from R and pseudoknot values are shown as (e), (f), (g) and (h).
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pone-0079288-g002: The distribution of R and pseudoknot parameters from positive and negative group of four IRES groups by VIPS analysis.The distribution of four IRES groups calculated by R and pseudoknot parameters in positive group and negative group. The R scores and pseudoknot scores were demonstrated according to IRES group 1 (a and e), IRES group 2 (b and f), IRES group 3 (c and g) and IRES group 4 (d and h). Linear discriminant analysis was applied to determine the cut-off line of the R score in each group shown as (a), (b), (c) and (d). Distribution of positive and negative IRES elements that were calculated and summarized from R and pseudoknot values are shown as (e), (f), (g) and (h).

Mentions: In order to develop a new IRES prediction system based on the previous IRES element search system (IRSS)[7], different standard templates and training data were inputted into VIPS which is ran by RNAL fold and RNA Align programs with length parameter (L = 250, default). The standard structures were fetched from four known groups of IRES elements based on Cricket paralysis virus (Group 1, accession number: AF218039), Hepatitis C virus (Group 2, accession number: AF177037), Encephalomyocarditis virus (Group 3, accession number: X74312.1) and Poliovirus (Group 4, accession number: V01148.1). Those standard IRES templates were applied into VIPS to calculate the appropriate individual R value and pseudoknot value from RNAL fold, RNA Align and pknotsRG programs. The R value of VIPS presents a score for match length (ALEN) divided distance score (DIST) that distributes into two separate groups, IRES-candidate group and negative group, when the cut-off value was determined [7]. For positive groups, all verified IRES elements (Table S1) of the four viral families (groups 1~4) fetched from NCBI GenBank (http://www.ncbi.nlm.nih.gov) and Rfam database (http://www.sanger.ac.uk/Software/Rfam/) were run through VIPS to calculate and classify into four IRES groups. Their R and pseudoknot values were collected as training data. For negative groups, the all known coding sequences without IRES elements of Poliovirus, Encephalomyocarditis virus, Hepatitis C virus and Cricket paralysis virus were input into VIPS to analyze their R and pseudoknot values. For each IRES group, the cut-off values were estimated from the positive group and negative group by linear discriminant analysis. The cut-off value is 1.61, 1.98, 1.87, and 1.58 of R value for IRES group 1, 2, 3, 4 respectively (Table 1; Figure 2a, 2b, 2c and 2d). The sensitivity and specificity of each IRES group are shown in Table 1.


Viral IRES prediction system - a web server for prediction of the IRES secondary structure in silico.

Hong JJ, Wu TY, Chang TY, Chen CY - PLoS ONE (2013)

The distribution of R and pseudoknot parameters from positive and negative group of four IRES groups by VIPS analysis.The distribution of four IRES groups calculated by R and pseudoknot parameters in positive group and negative group. The R scores and pseudoknot scores were demonstrated according to IRES group 1 (a and e), IRES group 2 (b and f), IRES group 3 (c and g) and IRES group 4 (d and h). Linear discriminant analysis was applied to determine the cut-off line of the R score in each group shown as (a), (b), (c) and (d). Distribution of positive and negative IRES elements that were calculated and summarized from R and pseudoknot values are shown as (e), (f), (g) and (h).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3818432&req=5

pone-0079288-g002: The distribution of R and pseudoknot parameters from positive and negative group of four IRES groups by VIPS analysis.The distribution of four IRES groups calculated by R and pseudoknot parameters in positive group and negative group. The R scores and pseudoknot scores were demonstrated according to IRES group 1 (a and e), IRES group 2 (b and f), IRES group 3 (c and g) and IRES group 4 (d and h). Linear discriminant analysis was applied to determine the cut-off line of the R score in each group shown as (a), (b), (c) and (d). Distribution of positive and negative IRES elements that were calculated and summarized from R and pseudoknot values are shown as (e), (f), (g) and (h).
Mentions: In order to develop a new IRES prediction system based on the previous IRES element search system (IRSS)[7], different standard templates and training data were inputted into VIPS which is ran by RNAL fold and RNA Align programs with length parameter (L = 250, default). The standard structures were fetched from four known groups of IRES elements based on Cricket paralysis virus (Group 1, accession number: AF218039), Hepatitis C virus (Group 2, accession number: AF177037), Encephalomyocarditis virus (Group 3, accession number: X74312.1) and Poliovirus (Group 4, accession number: V01148.1). Those standard IRES templates were applied into VIPS to calculate the appropriate individual R value and pseudoknot value from RNAL fold, RNA Align and pknotsRG programs. The R value of VIPS presents a score for match length (ALEN) divided distance score (DIST) that distributes into two separate groups, IRES-candidate group and negative group, when the cut-off value was determined [7]. For positive groups, all verified IRES elements (Table S1) of the four viral families (groups 1~4) fetched from NCBI GenBank (http://www.ncbi.nlm.nih.gov) and Rfam database (http://www.sanger.ac.uk/Software/Rfam/) were run through VIPS to calculate and classify into four IRES groups. Their R and pseudoknot values were collected as training data. For negative groups, the all known coding sequences without IRES elements of Poliovirus, Encephalomyocarditis virus, Hepatitis C virus and Cricket paralysis virus were input into VIPS to analyze their R and pseudoknot values. For each IRES group, the cut-off values were estimated from the positive group and negative group by linear discriminant analysis. The cut-off value is 1.61, 1.98, 1.87, and 1.58 of R value for IRES group 1, 2, 3, 4 respectively (Table 1; Figure 2a, 2b, 2c and 2d). The sensitivity and specificity of each IRES group are shown in Table 1.

Bottom Line: IRES elements have been applied as useful tools for bi-cistronic expression vectors.Current RNA structure prediction programs are unable to predict precisely the potential IRES element.This advance useful search approach for IRES structures will facilitate IRES related studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan.

ABSTRACT
The internal ribosomal entry site (IRES) functions as cap-independent translation initiation sites in eukaryotic cells. IRES elements have been applied as useful tools for bi-cistronic expression vectors. Current RNA structure prediction programs are unable to predict precisely the potential IRES element. We have designed a viral IRES prediction system (VIPS) to perform the IRES secondary structure prediction. In order to obtain better results for the IRES prediction, the VIPS can evaluate and predict for all four different groups of IRESs with a higher accuracy. RNA secondary structure prediction, comparison, and pseudoknot prediction programs were implemented to form the three-stage procedure for the VIPS. The backbone of VIPS includes: the RNAL fold program, aimed to predict local RNA secondary structures by minimum free energy method; the RNA Align program, intended to compare predicted structures; and pknotsRG program, used to calculate the pseudoknot structure. VIPS was evaluated by using UTR database, IRES database and Virus database, and the accuracy rate of VIPS was assessed as 98.53%, 90.80%, 82.36% and 80.41% for IRES groups 1, 2, 3, and 4, respectively. This advance useful search approach for IRES structures will facilitate IRES related studies. The VIPS on-line website service is available at http://140.135.61.250/vips/.

Show MeSH
Related in: MedlinePlus