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To compute the mutual bioisosteric similarity between two molecules a specific function has been derived that makes use of the alignment [5].
The degree of alignment quality that may be required by a user depends strongly on the intended use of the alignment, and AR alignments could certainly be used as a very good starting point for subsequent shape overlap optimization, e.g., using ROCS.
This motivates the use of the alignment in our MoRFpred.
It makes use of the alignment specificity of BLASTZ and the sensitivity of DIALIGN.
Ideally researchers could make use of the alignment of genomic sequence reads to the genome sequence assembly and the alignment of single molecule maps to the consensus genome maps to determine which assembly is likely to be incorrect.
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The efficiency of the programs used for the alignment of genome sequences can strongly improve the process of selection of human-specific SNPs.
We are aware that the SILVA alignment is not perfect and alignment errors may adversely affect results but the use of the original alignment allows for reproducibility.
This result holds true irrespective of the protein family identification method used and of the alignment software used (see fig. 1 and table 2).
The 5-μm-wide electrodes are used for the alignment of sparsely distributed nanotubes; the 3-μm-wide electrodes are used for the alignment of nanotube bundles and individual nanotubes.
DALI, a pairwise structural alignment algorithm [11], has been used for the alignment of protein domains with cupin fold.
The use of the KS alignment device allows accurate positioning of the femoral resurfacing component and produces results comparable to an image-free computer-aided system (Brainlab).
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