Methods of gene prediction

We saw in the previous chapter how prediction of CpG islands may be used to identify transcription start sites of protein-coding genes. However, there are many other elements and statistical properties of such genes that we may exploit for gene finding.

What are the methods available for computational gene finding? In general, one may distinguish between two major categories: de novo or ab initio methods and homology-based methods. The de novo methods make use of statistical signals in DNA sequences that are characteristic of protein-coding genes; the homology-based methods rely on the identification of exons by matching known mRNA or protein sequences or even profile HMMs to a genomic sequence. The homology-based methods are powerful but they require that mRNA or protein sequence information is available. Here we will focus on the de novo type of gene finding. What are the signals characteristic of proteincoding genes?