Global sequence searching

More recently a number of approaches have been proposed which combine the advantages of decision tree approaches (use of heterogeneous features, robustness to curse of dimensionality) and the HMM approach (statistical, global optimal search of sequences). In addition, there has been somewhat of a re-awakening of use of syntactic features due to the provision of more robust parsers. Rather than attempt an explicit model of prosodic phrasing based on trying to map from the syntax tree, most of these approaches use the syntax information as additional features in a classifier [508], [209], [257]. 

There are two approaches of sequence alignments A global alignment compares similarity across the full stretch of sequences, while a local alignment searches for regions of similarity in parts of the sequences. 

Fig. 1. A two-dimensional projection of the hyperdimensional fitness landscape. In this simplified representation, sequence space is shown for a 4-mer where the colors represent amino acid types. The all-blue sequence is the global optimum the lower fitness peaks are local optima. The problem of in vitro evolution is how to search this space effectively, without becoming trapped at a suboptimal fitness.

Deciding how to construct the input layer is application dependent. It is affected by many considerations. Should fixed-length sequence windows or variable-length sequences be used Is there a dependence on positional information Is it intended to search for signal or search for content What is the importance of local information or global information ... 

Signal peptide identification, like DNA intron/exon sequence discrimination, involves the two related problems of signal peptide discrimination (search for content) and cleavage site recognition (search for signal). It is well suited to neural network methods for several reasons. The functional units are encoded by local, linear sequences of amino acids rather than global 3-dimensional structures (Claros et al., 1997). The ambiguity of... 

Figure 22 illustrates how relatively simple global quality factors can be used as filters in the search for optimum solutions in the parameter space that defines multiple-pulse sequences. Suppose for typical coupling constants = 10 Hz a multiple-pulse sequence with a constant rf amplitude = 10 kHz is desired that effects efficient Hartmann-Hahn transfer in the offset range of +4 kHz. Here, the simple two-dimensional parameter... 

---