Phylogenetic trees  (Page 2/3)

The Tree of Life is an example of a cladogram illustrating the relationships between taxa, based on the collective evidence from many different fields of biology and bioscience. In contrast, the subject of this tutorial is the construction of cladograms through bioinformatics tools, where the cladograms are based on sequence data. First, use the Biology Workbench (2) to build a simple unrooted cladogram. The Workbench will require a password (it's free), but it will grant entrance immediately upon registration of a password. Enter the site, and scroll down the page until the five menu buttons are visible. The "Session Tools" button allows the naming of a session, so that different jobs in progress can be saved under distinct sessions. Select "Session Tools", then select "Start New Session" and click on "Run" to change the name of "Default Session" to a new name. Once the workbench has been exited, the session will remain. Subsequently, clicking on the dot to the left of the session name under the "Session Tools" menu, and then selecting "Resume Session", will recall the session. The Workbench policy at the time of this writing is that old jobs are deleted only when an account has not been accessed for 6 months.

Next, select "Protein Tools" from the menu buttons, highlight "Ndjinn Multiple Database Search", and click "Run". In the query box to the right of the term"Contains", type HSP70, for the molecular chaperone, heat shock protein 70 kDa. Scroll down the database list and check the box to the left of the databaseentitled "PDBFINDER" before hitting the "Search" button. Among the results, find 2BUP, chaperone, and check the box to the left. Then select the menubutton entitled "Import sequence(s)". This will import the sequence in fastA format into the open session. Now, under the box of session options, thereshould be a listing for the 2BUP sequence, with a small box to the left. Notice that the main menu under "Protein Tools" allows more options such as"Delete Protein Sequence", "Copy Protein Sequence" and "Add New Protein Sequences". For now, select the "Ndjinn Multiple Database Search" again.Search the PDBFINDER Database again by scrolling down the page and selecting it, but this time, just search using the PDB ID codes 1HKB, 1ATN and 1DKG forhexokinase, actin and the molecular chaperone DnaK (use the OR operator between each PDB ID code to search for all three in the same search).Import all three sequences simultaneously by checking the box to the left of the PDB ID codes used in the query and clicking on "Import sequence(s)".1DKG will return three chains, A, B and D. Only chain D is the molecular chaperone, chains A and B are nucleotide exchange factors that co-crystallizedwith DnaK. Delete chains A and B by checking the box to the left of 1DKG_A and 1DKG_B, highlighting "Delete Protein Sequence", and clicking on "Run".Actin (1ATN) returns two chains, but chain A is the actin, chain D should be deleted in the same manner. Hexokinase (also called phosphotransferase) will return two chains as well. They are both hexokinase, but two identical sequences are not desirable in thecladogram, so delete chain B. Four sequences should remain, 1DKG_D, 1ATN_A, 1HKB_A, and 2BUP_A; check the boxes to the left of each of these. Scroll down the protein tools menu and highlight "CLUSTALW - Multiple Sequence Alignment", then click "Run". The default parameters will be sufficient for our purposes, just select "Submit". When the sequence alignment is returned, scroll down the page and view the multiple alignment. The Workbench automatically returns an unrooted tree with the alignment. Look at the unrooted tree.