One thing to note is that in order for this strategy to work, researchers need to compare organisms that are not too similar or different. Comparing yeast genome to human genome would reveal genes which serve only very simple functions, i.e. are responsible for the processes of only one cell. On the other hand, comparing human genome to chimp genome would not reveal any genes because the genomes are 90% similar, so everything is conserved. Thus a good phylogenetic scope is needed to produce good result.
Figure 15. This shows sequence comparison between the genomes of different species. The
red line shows the level of conservation in different regions. Exons are represented as purple blocks -- note the high level of conservation. Further, observe that the top plot shows
comparison between 8 different species, the second plot – between 6, and the bottom one – between 5. Note the differences in the level of conservation of other regions of the genomes
besides the exons.
Finally, looking for patterns of conservation can not only help predict genes, but also give insight into the functions of these genes. For example, if a gene is conserved between yeast and human genomes, it means that the gene is not related to a body plan, or to any other human characteristic that yeast lack. Thus sequence comparison and other comparative studies between different organisms is key to finding genes, determining function, and uncovering the steps that lead to the evolution of one organism from the other.
2. Sequence Comparison and Alignment
Thus, as described above, gene prediction motivates the problem of sequence comparison. Simply put, the goal of sequence alignment is to put in gaps between letters of two or more desired sequences as to reveal sequence similarity. This is best illustrated by a diagram.
Figure 16. Given the two sequences above, sequence alignment attempts to insert gaps, as shown below, to reveal similarity between the two sequences, as highlighted in dark blue.