Alignment gaps

Fig. 4.2. Schematic diagram of the components of the IGSs for three species of Schistosoma, after Kane and Rollinson (1998). Major repeats are shown as open boxes, with an arrowhead indicating whether each is direct or inverted. Repeats coded by the same letter are similar in sequence. The AT rich region (present in Schistosoma intercalatum and S. haematobium) is shown as a filled box. Breaks in the horizontal line indicate large alignment gaps.

When no gap penalty is used then the Needleman-Wunsch alignment may contain a largt unrealistic number of gaps. The simplest type of gap penalty (other than not to have one) i to use a length-dependent scheme in which one assigns a fixed negative value for each insertio ... 

Fig. 10.16 Finding the optimal sequence alignment using dynamic programming with a scoring scheme in which a match scores 1, a mismatch scores —1 and the gap penalty is —2.

Gap A break in a DNA or protein sequence which enables two or more sequence to be aligned... 

Radiographic tests are made on pipeline welds, pressure vessels, nuclear fuel rods, and other critical materials and components that may contain three-dimensional voids, inclusions, gaps or cracks that are aligned so that the critical areas are parallel to the x-ray beam. Since penetrating radiation tests depend upon the absorption properties of materials on x-ray photons, the tests can reveal changes in thickness and density and the presence of inclusions in the material. 

Often a failure on a fault may be due not to the inadequate size of busbars, fasteners or insulators but to poor alignment of the insulators or to too large a gap between the busbar and the insulator slots. It may be a consequence of an inappropriate mounting or unequal width of the busbars or insulator slots. In such cases, load sharing w ill be uneven and the weakest section may fail. This can be illustrated as follows ... 

Figure 4 Sample spatial restraint m Modeller. A restraint on a given C -C , distance, d, is expressed as a conditional probability density function that depends on two other equivalent distances (d = 17.0 and d" = 23.5) p(dld, d"). The restraint (continuous line) is obtained by least-squares fitting a sum of two Gaussian functions to the histogram, which in turn is derived from many triple alignments of protein structures. In practice, more complicated restraints are used that depend on additional information such as similarity between the proteins, solvent accessibility, and distance from a gap m the alignment.

WR Taylor. Multiple protein sequence alignment Algorithms and gap insertion. Methods Enzymol 266 343-367, 1996. 

Zhu et al. [15] and Liu and Lawrence [61] formalized this argument with a Bayesian analysis. They are seeking a joint posterior probability for an alignment A, a choice of distance matrix 0, and a vector of gap parameters. A, given the data, i.e., the sequences to be aligned p(A, 0, A / i, R2). The Bayesian likelihood and prior for this posterior distribution is... 

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