DNA+Data+Analysis

__Data Analysis __
The results obtained from the tools BLAST, MEGA, Gene Oncology, and NCBI Map Viewer were used to investigate the following research question: If the amelogenin gene is found in other species can another function be found other than sex determination? If the amelogenin gene, or protein, is found in other species it might allow for investigators to research other genes that could help with disaster victim identification. The results from BLAST were used to obtain genes and proteins that were similar to the gene and protein investigated. The gene investigated was AMELY amelogenin, Y-linked [ Homo sapiens (human) ], NC_000024.9. There was not a large variety of species that had the same gene that was similar to AMELY for Human. The query covers and identity percentage of the similar genes listed from the BLASTn results were not very high. The genes chosen to use for the alignment either were not a good alignment or there was an error in the MEGA program, because a DNA sequence alignment for the selected genes was unable to be obtained. After the parameters of the ClustalW DNA alignment were selected, the program began the process of aligning the genes, but every time it froze halfway through loading the alignment. The alignment was probably too much for the program, so it was unable to load. Phylogenetic trees were unable to be obtained for the AMELY gene because the alignment was never obtained. There were a wide variety of species that had similar sequences to the Amelogenin, Y-linked [Homo sapiens], EAW59129.1 protein that were obtained from the BLASTp results. The alignment retrieved from the similar proteins chosen displayed a very good protein alignment because the protein sequences were very similar. The phylogenetic trees displayed in the results are the Minimum Evolutionary Tree and the Maximum Parsimony Tree. The minimum evolutionary tree was used in the results because its bootstrap values were over 60, which means that the alignment for this tree was very good. The minimum evolution tree shows how much of the protein sequence is similar between the organisms. This answers part of the research question that there are other species with similar proteins that can be investigated. The maximum parsimony tree shows the similarities in the protein’s pathways and functions between the different organisms. The bootstrap values in the maximum parsimony tree were all over 60, which means that the alignment was good for this phylogenetic tree. This indicates that the amelogenin protein has similar functional properties in these species. The phylogenetic trees for the maximum likelihood tree, neighbor-joining tree and UPGMA tree were not presented in the results because they all had bootstrap values under 60. This indicates that the alignment was not good for these types of phylogenetic trees and is therefore irrelevant for this investigation.  The overall investigation completed to answer the research question, on whether there are any other functions of the amelogenin Y-linked gene or protein that can help with victim identification, was successful. The results from BLAST and MEGA indicate that there are a variety of species that have similar amelogenin protein sequences. The Gene Ontology tool indicates that the amelogenin gene has a biological process of multicellular organismal development, which indicates that the amelogenin gene is responsible for development of the sex determining organs in organism development. The NCBI Map Viewer tool indicates that the amelogenin gene on chromosome Y is in the same location in humans and primates. These results give evidence that there are other species with the similar amelogenin gene and protein sequences, however they seem to have the same function of sex determination. The result of amplifying the amelogenin gene in a disaster victim is only sex determination. It is recommended in future investigations to sequence a different gene that is located close to the amelogenin gene.

Next Page: Work Cited Homepage: DNA Profiling