Codon bias detection

Translation initiation site. In eukaryotes, if the transcription start site is known, and there is no intron interrupting the 5 UTR, Kozak s rule (Kozak, 1996) probably will locate the correct initiation codon in most cases. SpUcing is normally absent in prokaryotes, yet because of the existence of multicitronic operons, promoter location is not the key information. Rather the key is reUable localization of the ribosome binding site. The TATA sequence about 30 bp from the transcription start site may be used as a possible resource. 

Termination signals. The polyadenylation and translation termination signals also help to demarcate the extent of a gene (Fickett and Hatzigeorgiou, 1997). 

1 Expression profiling DNA chips [Adapted from Schena2003] 

The widespread use of PCR amplification in microarray manufacture places much importance on the availability of informatics tools for automated primer design. A primer is a synthetic oligonucleotide that hybridizes to a complementary nucleic acid template, and expedites (primes) enzymatic synthesis by providing a starting point for enzyme. PCR primers bind to proximal and distal sites on cDNA templates, allowing target sequences 

TABLE 15.11 Factors affecting hybridization in DNA microarray analysis 

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