This chapter contains sections titled:

• Structural Organization and Expression of Eukaryotic Genes

• Methods of Functional Signal Recognition

• Linear Discriminant Analysis

• Prediction of Donor and Acceptor Splice Junctions

• Identification of Promoter Regions in Human DNA

• Recognition of PolyA Sites

• Characteristics for Recognition of 3′-Processing Sites

• Identification of Multiple Genes in Genomic Sequences

• Discriminative and Probabilistic Approaches for Multiple Gene Prediction

• Internal Exon Recognition

• Recognition of Flanking Exons

• Performance of Gene Identification Programs

• Using Protein Similarity Information to Improve Gene Prediction

• Genome Annotation Assessment Project (EGASP)

• Annotation of Sequences from Genome Sequencing Projects

• Characteristics and Computational Identification of miRNA genes

• Prediction of microRNA Targets

• Internet Resources for Gene Finding and Functional Site Prediction

• Acknowledgments

• References