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If both alignment methods were able to align a molecule, and their aligned locations were similar (within half the length of the molecule), a consensus was reached, and we included the OMBlast result in our integrated list.
Different alignment methods were compared including the classic (PCA), normal PCA (NPCA), and our method.
Based on the co-crystallized compound (PDB ID: 1UWJ), several alignment methods were utilized to derive reliable CoMFA and CoMSIA models.
The results of each individual phylogenetic analysis are shown in Figure 3. Regardless of whether amino acid or nucleotide sequence data was analyzed, or which of the two alignment methods were utilized, striking concordance was found to exist among the three phylogenetic inference methods.
To address these challenges, pairwise alignment methods were developed to utilize less computational resources [ 6- 8].
Network alignment methods were initially developed for protein interaction networks [ 22].
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In this paper, the hardware and the software alignment are described, and the track-based alignment methods are explained in detail.
The selected alignment methods are analyzed in terms of their computational complexity and the estimates of numbers of arithmetic operations for each method are given.
The reconstructed images from cross-correlation and our alignment methods are shown in Figure 4.
Comparisons with state-of-the-art range-bin alignment methods are included and advantages of the proposal are highlighted.
Alignment methods are often impaired by "false predictions" caused by the ubiquitously present short sequences throughout the genome.
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