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FRASS: the web-server for RNA structural comparison.

Kirillova S, Tosatto SC, Carugo O - BMC Bioinformatics (2010)

Bottom Line: The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank.Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Structural and Computational Biology, Max F Perutz Laboratories, Vienna University, Campus Vienna Biocenter 5, A-1030 Vienna, Austria. sviatlana.kirylava@univie.ac.at

ABSTRACT

Background: The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.

Results: The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.

Conclusions: The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

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Related in: MedlinePlus

The ROC curves. The solid line represents the curve computed for 789 RNA chains taken from the DARTS classification (AUC = 0.75). The dashed line was obtained by using the NR95-SCOR dataset (AUC = 0.86).
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Figure 5: The ROC curves. The solid line represents the curve computed for 789 RNA chains taken from the DARTS classification (AUC = 0.75). The dashed line was obtained by using the NR95-SCOR dataset (AUC = 0.86).

Mentions: Figure 5 shows the ROC curves obtained as described above. The areas under ROC curves (AUC) are 0.75 and 0.82, respectively for the DARTS and SCOR classifications. These values monitor the performance of the method. A value equal to 0.50 would be associated with a random similarity measure, while a value equal to one would be obtained with an impeccable similarity measure. The AUC values obtained in the present study compare well with those obtained with the DIAL [13], SARSA [15], and SARA [16] methods, which range from 0.58 to 0.86 depending on which benchmarking set is used and on the fine tuning of each method.


FRASS: the web-server for RNA structural comparison.

Kirillova S, Tosatto SC, Carugo O - BMC Bioinformatics (2010)

The ROC curves. The solid line represents the curve computed for 789 RNA chains taken from the DARTS classification (AUC = 0.75). The dashed line was obtained by using the NR95-SCOR dataset (AUC = 0.86).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2902451&req=5

Figure 5: The ROC curves. The solid line represents the curve computed for 789 RNA chains taken from the DARTS classification (AUC = 0.75). The dashed line was obtained by using the NR95-SCOR dataset (AUC = 0.86).
Mentions: Figure 5 shows the ROC curves obtained as described above. The areas under ROC curves (AUC) are 0.75 and 0.82, respectively for the DARTS and SCOR classifications. These values monitor the performance of the method. A value equal to 0.50 would be associated with a random similarity measure, while a value equal to one would be obtained with an impeccable similarity measure. The AUC values obtained in the present study compare well with those obtained with the DIAL [13], SARSA [15], and SARA [16] methods, which range from 0.58 to 0.86 depending on which benchmarking set is used and on the fine tuning of each method.

Bottom Line: The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank.Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Structural and Computational Biology, Max F Perutz Laboratories, Vienna University, Campus Vienna Biocenter 5, A-1030 Vienna, Austria. sviatlana.kirylava@univie.ac.at

ABSTRACT

Background: The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.

Results: The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.

Conclusions: The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

Show MeSH
Related in: MedlinePlus