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As shown above, the incorporation of LSPPs can significantly improve both alignment accuracy and sensitivity of fold recognition.
Experimental results indicate that our algorithm greatly outperforms the others in terms of both alignment accuracy and running time.
This motivates us to develop a new method for global network alignment to significantly improve both alignment accuracy and computational efficiency.
Combined with our context-specific local alignment potential, our distance-based pairwise potential can help improve both alignment accuracy and template selection especially for hard targets.
We have tested HubAlign on both prokaryotic and eukaryotic PPI networks, showing that HubAlign greatly outperforms several popular methods such as IsoRank, MI-GRAAL, GHOST and PISwap in terms of both alignment accuracy and running time.
Extensive performance evaluation on protein alignment benchmark datasets shows that the proposed message-passing scheme clearly outperforms the traditional pair-HMM-based approach, in terms of both alignment accuracy and computational efficiency.
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Based on testings on three public benchmarks, we have shown that the incorporation of the two terms improves both the alignment accuracy and recognition sensitivity in fold recognition.
Although under some circumstances, the choice of phylogenetic inference method is known to have a major effect on phylogenetic accuracy [ 34], previous studies have shown that both alignment accuracy [ 35- 37] and the ratio of phylogenetic signal to noise in the alignment [ 38] can be even more important than the choice of phylogenetic method.
The proposed message-passing scheme effectively addresses a number of limitations of the traditional pair-HMM-based approach, and extensive performance assessment based on BAliBASE 3.0 shows that the proposed scheme consistently outperforms the pair-HMM approach, both in terms of alignment accuracy and computational efficiency.
Results: Compared with other aligners, Slider has higher alignment accuracy and efficiency.
The comparison in this section consists of the alignment accuracy and robustness.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com