Comparing the amino acid sequences using clustalw

After collecting the related species information for a particular protein you should be returned to the session page with your choices now showing. Check the boxes of related molecules you want to use and click the CLUSTALW box. A new page appears and allows you to alter some parameters of the Workbench and change the pull down menu for the guide tree display to rooted and unrooted trees . Submit this to the workbench.

Clustalw is an alignment tool that compares the sequences of the amino acids in the chosen organisms and aligns them by their portions of similar sequence order. The next page shows a few things, the aligned amino acids that are similar will be colored in blue (fully conserved) or green (semi-conserved) for the parts that are most similar. Conservation is a property that shows identical or nearly identical portions of the molecule. These tend to show important structural areas of the protein that need to be maintained for proper function. Conversely the areas of dissimilarity are where the evolution happens. Due to their location they don’t tend to affect the function, yet show where changes have occurred. These changes are what help determine the shape of the trees.

Note: If you notice any apparent oddities to the trees, check to see if the same portions of the molecule are being compared (alpha vs. beta, tentative analyses vs. validated). Also, when using several proteins don’t clustalw them together.

Rooted trees are projected from the side rather than the ground but if you take the monitor and lay it on its side they will look just fine. (JUST KIDDING! LEAVE THE MONITOR ALONE!) There is actually a wraparound effect that can occur with two groups on opposite sides of the tree actually being closely related. This is related to the problem of trying to generate trees for a 2-Dimentional monitor screen from what is more of a 3-Dimentional analysis of branching patterns.

Unrooted trees are pictured like a branching tree as if you were looking at it from above. This can sometimes provide the greatest insight into the divergence of groups of organisms.

Generating a composite cladistic or phylogenic tree.

After gathering the various trees generated by Biology Workbench program try to find similar organisms between these data.

Generating a composite tree means you need to place the differing analyses for the organisms into one tree. To combine the trees you produced with BW look for similar organisms in the diagrams. Overlapping the one data set into the other is one way to make a bigger tree. However, there are problems that may arise, some organisms may appear on differing branches in different protein analyses. They may be linked in one but on a completely different branch in another. What might cause this problem and what might be done to resolve the discrepancy to make the most accurate tree?