Bioinformatics in Molecular Anthropology

Using Python Language to Analyze DNA of Primates in order to Study Evolution

Chanel LigonMentor : Dr. Todd DisotellCo-Mentor : Christina BergeyNYU Anthropology Department

Bio Informatics

Advances in genomic technologies has led to an explosive growth in the biological information. Bioinformatics is the application of information technology to the field of molecular biology.

Purpose/Goals

To find the region of Mitochondrial DNA with the most variation in the group of primates Catarrhines.

To learn how to use Python script to generate programs that compare base pairs and add up all the differences.

Importance of Mitochondrial DNA vs. Nuclear DNA

We use Mitochondrial DNA rather than Nuclear DNA of the body because mitochondrial DNA is maternal. Meaning it comes only from the mother so its much clear the origin of the species.

Mitochondrial DNA is much rather used then nuclear DNA because with mitochondrial DNA scientists are able to look within the cells of a living organism and analyze short loops of genetic code. Mitochondrial DNA has also allowed scientists to trace back the evolution and migration of human species.

Catarrhines

The group Catarrhini includes Old World monkeys, apes, and, humans, all of which evolved in the Old World tropics.

It consist of Old World monkeys , Gibbons , Orangutans , Gorillas , Chimpanzees , and Humans.

Python Script & Language

Python script is a substantially powerful dynamic programming language that is used in a large variety of application domains.

Our Program

Also the purpose was to learn how to use Python script to generate programs that compare base pairs and add up all the differences in each primate group. The program was created so that it would hold a function to count number of differences in two strings of DNA , generates coordinates for DNA substrings , and also compares DNA in pairs and writes the matrix to a file.

Running the Program

Because of the large quantity needed to be compared the program could take up to 24 hours to run.

Using a larger computer will help it run much faster.

Results

When the programmed finished running and we placed the data into a spreadsheet my inference was correct. The graphs showed variation between each comparison. When we created the program we made a part in which it would ask “What size window would you like to use?” The higher the number you put in the less variation you would find because the DNA as a whole is very similar. The smaller number you put in , for example five hundred , you will get more of a variation because there are less base pairs to look at and compare and also its not such a large bulk.

Importance of Studying DNAIt is important to study

DNA in order to understand evolution because when analyzing DNA using bioinformatic approaches it reveals a number of interesting patterns in primates and their history.

Conclusion

This course helped me understand topics such as computer programming, molecular phylogeny, and data-mining. It also helped me gain a competency in programming in the Python language.

In the future we hope to work with different kind of programming languages such as Java. That we may find to be quicker and more efficient.

References http://www.mygenetree.com/images/img-mitochondrial-dna.jpg

python.org

linux.org

ubuntu.com

Connect : Information Technology at NYU Spring/Summer 2008 ; 20-23 Dr. Todd Disotell , Dr. Anthony Di Fiore

http://anthro.palomar.edu/primate/prim_5.htm

http://ghr.nlm.nih.gov/chromosome=MT

http://www.christinabergey.com/bioinfo/

http://www.ncbi.nlm.nih.gov/

The Birth of Complex Cells :Scientific American , April 1996

Science & Society , Human Origins : The molecular perspective , Stoneking , Mark , VOL 9

Acknowledgements

Mentor : Dr. Todd Disotell

Co-Mentor: Christina Bergey

Harlem Children Society

Harlem Children Society Staff

Dr. Sat Bhattacharya