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IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico.

Wu TY, Hsieh CC, Hong JJ, Chen CY, Tsai YS - BMC Bioinformatics (2009)

Bottom Line: We designed an IRES search system, named IRSS, to obtain better results for IRES prediction.Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted structures.After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan. tywu@cycu.edu.tw

ABSTRACT

Background: Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal with IRES elements.

Results: We designed an IRES search system, named IRSS, to obtain better results for IRES prediction. RNA secondary structure prediction and comparison software programs were implemented to construct our two-stage strategy for the IRSS. Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted structures. After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters.

Conclusion: IRSS is freely available at this website http://140.135.61.9/ires/. In addition, all source codes, precompiled binaries, examples and documentations are downloadable for local execution. This new search approach for IRES elements will provide a useful research tool on IRES related studies.

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Web-based IRES search system. (A) Input window, sequences as FASTA or plain text formats. (B) The example of output data. All of the results with R scores higher than 1.5 after IRSS prediction can be listed. Those data include potential IRES sequences, potential secondary structures and predicted minimum free energies.
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Figure 4: Web-based IRES search system. (A) Input window, sequences as FASTA or plain text formats. (B) The example of output data. All of the results with R scores higher than 1.5 after IRSS prediction can be listed. Those data include potential IRES sequences, potential secondary structures and predicted minimum free energies.

Mentions: The IRSS tool is available in web-based on line search as . The original RNA prediction software and perl-script programs, such as RNAL fold, RNA Align, UTR2SQ.pl...etc., have been transferred into Web service style and executed automatically. Figure 4 showed the input window and output example. The input sequences can be FASTA and/or plain text formats and results are in pain text which is able to be read by any word processing software. The default L parameter of web-based IRSS is 250 and R value is 1.4. The IRSS web tool is run in a Linux workstation which has Fedora 6.0 operation system.


IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico.

Wu TY, Hsieh CC, Hong JJ, Chen CY, Tsai YS - BMC Bioinformatics (2009)

Web-based IRES search system. (A) Input window, sequences as FASTA or plain text formats. (B) The example of output data. All of the results with R scores higher than 1.5 after IRSS prediction can be listed. Those data include potential IRES sequences, potential secondary structures and predicted minimum free energies.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2698906&req=5

Figure 4: Web-based IRES search system. (A) Input window, sequences as FASTA or plain text formats. (B) The example of output data. All of the results with R scores higher than 1.5 after IRSS prediction can be listed. Those data include potential IRES sequences, potential secondary structures and predicted minimum free energies.
Mentions: The IRSS tool is available in web-based on line search as . The original RNA prediction software and perl-script programs, such as RNAL fold, RNA Align, UTR2SQ.pl...etc., have been transferred into Web service style and executed automatically. Figure 4 showed the input window and output example. The input sequences can be FASTA and/or plain text formats and results are in pain text which is able to be read by any word processing software. The default L parameter of web-based IRSS is 250 and R value is 1.4. The IRSS web tool is run in a Linux workstation which has Fedora 6.0 operation system.

Bottom Line: We designed an IRES search system, named IRSS, to obtain better results for IRES prediction.Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted structures.After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan. tywu@cycu.edu.tw

ABSTRACT

Background: Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal with IRES elements.

Results: We designed an IRES search system, named IRSS, to obtain better results for IRES prediction. RNA secondary structure prediction and comparison software programs were implemented to construct our two-stage strategy for the IRSS. Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted structures. After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters.

Conclusion: IRSS is freely available at this website http://140.135.61.9/ires/. In addition, all source codes, precompiled binaries, examples and documentations are downloadable for local execution. This new search approach for IRES elements will provide a useful research tool on IRES related studies.

Show MeSH