Exercise 1. Having found and described mutations on DNA sequences, now you should have a look at the possible structural or functional effects that mutations could have on the protein encoded by the gene. Many of the algorithms in use in ‘linear’ bioinformatics refer to linear sequences. A lot of interesting information can be extracted using these tools, as you will find if you follow these steps.

• Open Swissprot main page through the link above and enter the ID number for human rhodopsin. Notice the literature references where the original work was published.
• Search the contents of Swissprot for proteins of matching sequence using the ‘Quick BlastP search’ button on the top right of the page. Notice the apparent extraordinary conservation of structure throughout the zoological scale. Notice the different headings under which you could search the proteins retrieved, in particular the taxonomic view. As a possible project using this facility, you could compare the rhodopsins from vertebrate species that live in very different light conditions, such as a nocturnal mouse, or a deep sea fish, and a diurnal tropical bird or mammal predator that work in intense light. The working hypothesis here would be that selection would have optimized these molecules for their respective habitats, so any minor sequence differences may be responsible for such refinements.
• In particular, select the two proteins of interest here, ie. bovine and human, and observe their alignment running ClustalW. List their differences in table form. Are the aminoacids replaced by other aminoacids of similar properties, or different? You could consult the ‘Aminoacid Information Resource’ for this.
• Open the Iowa table database listing human rhodopsin mutations associated with ADRP and plot the aminoacid substitutions on the human sequence, observing again the type of aminoacid substitution.