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Based on the co-crystallized compound (PDB ID: 1UWJ), several alignment methods were utilized to derive reliable CoMFA and CoMSIA models.
Essoussi et al. compared several alignment tools, indicating that no single tool can consistently outperform other ones by the estimation of quality alignment [35].
In the longer term we are working on improving various aspects of usability, specifically the ability to run several alignment jobs concurrently, with the provision of session identifiers such that users can quickly retrieve results of runs, as well as email notifications of run completion.
Tentacle can use several alignment algorithms.
LT identified and corrected several alignment errors and incomplete gene sequences.
Other methods use several alignment features as evidence of an indel.
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The raw sequencing data can in turn have several alignments associated, for example, using different aligners or alignment configurations.
Several alignments of the aftershock hypocenters corresponding to the fault planes of the main shock can be recognized.
Because most information at the DNA level is maintained in the coding regions of shared orthologues, it leads to little loss of information to use the translated peptides to conduct local similarity searches [55], [56], this have lead to development of several alignment-free distance and similarity metrics as well as phylogenetic reconstruction methods [49], [50], [51], [52], [53], [54].
To compare intron positions we used several alignments with Clustal W (www.ebi.ac.uk/) or at NPS Web server (http://npsa-pbil.ibcp.fr).ibcp.fr
Although other methods, such as DALI [32] and CE [33], can simultaneously make several alignments with statistical Z-scores, most of them are local/partial alignments.
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