Yesterday Graham introduced Clare and I to BLAST, we learned how to use BLAST to identify sequences and in species identification. This is only step 1.
Species identified and similarities with other species identified but you now must use the sequence and in the Bat lab the production of a phylogenetic tree is the goal.
Phylogenetic trees (gene trees which should an evolutionary pathway) are constructed using Homologs ( the sequences must have descended from a common ancestor) BLAST helps you pick sequences that could be used in the tree construction. Each sequence that appears when you do a BLAST analysis will have an ‘e’ value- values of less than e -5 are accepted as Homologs and can be used in alignment.
Selected the Homologs and input them into a program that aligns them, it places them underneath each other trying to match the sequences with best fit, creating spaces to achieve this fit.
This is all done on the computer using free tool such as MEGA but mainly Clustal X. This is the beginning of the tree creating process.
Did you know that Clustal X is one of the most widely cited scientific publications in the history of biology. Des Higgins in UCD one of its creators is one of the most cited computer scientists in the world!
Intense morning with slow laptops and programmes (MEGA) slowing as the scientists on the other side of the planet log on. Learned a lot and trying to study theory to help paint the picture.