Applications - Nucleic Acid Sequence Analysis

The identification and analysis of other signals, binding sites or regulatory sites, such as promoters, ribosome-binding sites, and transcriptional initiating and terminating sites 

Other applications of neural networks are sequence classification and feature detection 

Snyder Stormo, 1993 I/E Feature Weighting 2L/FF/Delta Feat6/l(hiequality) 

Snyder Stormo, 1995 I/E Feature Weighting 2,3L/FF/Delta,BP Feat6/l(Inequality)  

Stormo et al., 1982 Ribosome Binding Site Perceptron BIN4/1(Y,N) 

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Chapter 9 Applications - Nucleic Acid Sequence Analysis 05... 

Table 9.1 Neural network applications for nucleic acid sequence analysis.

Sequence similarity database searching and protein sequence analysis constitute one of the most important computational approaches to understanding protein structure and function. Although most computational methods used for nucleic acid sequence analysis are also applicable to protein sequence studies, how to capture the enriched features of amino acid alphabets (Chapter 6) poses a special challenge for protein analysis. 

Applications of the PCR technique include 1) efficient comparison of a normal cloned gene with an uncloned mutant form of the gene, 2) detection of low-abundance nucleic acid sequences, 3) forensic analysis of DNA samples, and 4) prenatal diagnosis and carrier detection, for example, of cystic fibrosis. 

The application of in situ hybridization (ISH) has advanced from short lived, non-specific isotopic methods, to very specific, long lived, multiple color fluorescent-ISH probe assays (FISH). Improvements in the optics, filter technology, microscopes, cameras, and data handling by software, have allowed for a cost effective FISH setup to be within reach of most researchers. The application of mFISH (multiplex-FISH), coupled to the advances in digital imaging microscopy, have vastly improved the capabilities for non-isotopic detection and analysis of multiple nucleic acid sequences in chromosomes and genes (1). 

Nucleic acids are also valuable as diagnostic reagents. In combination with the recently developed amplification method, polymerase chain reaction (PCR), nucleic acid probes allow the detection of trace amounts of a specified nucleic acid sequence. Thus, the presence of the DNA of pathogens can be ascertained with great sensitivity and rapidity. Further, these tools permit the analysis and the detection of gene defects in individual patients, and aid in the tailoring of therapeutic strategies. These applications are discussed in Chapter 8. 

Stone, T and Durrant, I. (1991) Enhanced chemiluminescence for the detection of membrane bound nucleic acid sequences, in Genetic Analysis Techniques and Applications 8,230-237... 

The investigations directed at the synthesis of thymine-substituted polymers demonstrate that the type of functional groups displayed by nucleic acid bases are compatible with ROMP. Moreover, the application of MALDI-TOF mass spectrometry to the analysis of these polymers adds to the battery of tools available for the characterization of ROMP and its products. The utility of this approach for the creation of molecules with the desired biological properties, however, is still undetermined. It is unknown whether these thymine-substituted polymers can hybridize with nucleic acids. Moreover, ROMP does not provide a simple solution to the controlled synthesis of materials that display specific sequences composed of all five common nucleic acid bases. Nevertheless, the demonstration that metathesis reactions can be conducted with such substrates suggests that perhaps neobiopolymers that function as nucleic acid analogs can be synthesized by such processes. 

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