Sequence discrimination

The precise manner in which proteins with zinc fingers bind to DNA differs from one protein to the next. Some zinc fingers contain the amino acid residues that are important in sequence discrimination, whereas others appear to bind DNA nonspecifically (the amino acids required for specificity are located elsewhere in the protein). Zinc fingers can also function as RNA-binding motifs—for example, in certain proteins that bind eukaryotic mRNAs and act as translational repressors. We discuss this role later (Section 28.3). 

A. J. Doherty, A. F. Worrall, and B. A Connolly. Mutagenesis of the DNA binding residues in bovine pancreatic DNase 1 An investigation into ihe mechanism of sequence discrimination by a sequence selective nuclase Nucleic Acids Res. 19 6129-6132 (1991). 

Sequence Discrimination/ Feature Detection/ Classification/ Structure Prediction... 

The direct sequence encoding methods preserve the order of residues along the sequence string and encode primarily local information. They are, however, not suitable when global sequence features or information content is more important to the application, or when variable length sequences are to be analyzed. This is evident in the intron/exon sequence discrimination (e.g., Uberbacher Mural, 1991 Snyder Stormo, 1993) and protein classification (e.g., Wu et al., 1992 Ferran Ferrara, 1992) problems. 

The next issue of evaluation mechanism is to define a measure for the quality of a particular prediction. For sequence discrimination problem, which involves a yes or no answer (e.g., binding or non-binding, member or non-member), the performance can be measured by sensitivity, specificity, positive predictive value, negative predictive value, accuracy, and correlation coefficient, as shown in... 

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... 

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