Point-based alignment

Virtual screening often benefits from an expert bias which helps focus on more desirable results, given in the form of additional information. A point in case is docking under pharmacophore constraints [37] or the concept of relative pharmacophores with a special internal reference point [38]. Yet another application for a directionally biased compound comparison is the selection of chemical reagents where functional attachment points are aligned and pharmacopho-ric features are examined relative to this point of reference by a procedure termed GaP [39]. Other concepts which try to describe combinatorial products in terms of their educts and need a special reference point are shape-based To-pomers [24] and pharmacophore based OsPreys [40]. 

Another algorithm, Perseus, approaches chimera detection without the use of databases. It instead identified chimeras based on the observation that chimeric sequences should undergo one less PCR cycle than its parent strands, and thus the parent strands should be at least equal in frequency to the chimeric strands. Perseus then compares each sequence to every sequence with equal or greater frequency in order to identify a set of potential parents and break points. Based on the three-way alignment data, an optimum chimera is calculated. If the distance from the sequence to the optimum chimera is less... 

Measurements taken with this device are based on a point of reference at the zero position, which is defined as the alignment fixture at the top of the shaft - referred to as the 12 o clock position. In order to perform the alignment procedure, readings also are required at the 3, 6, and 9 o clock positions. 

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