Websites/Datasets Used

 

Many websites and scholarly papers were used as references and analysis for this project.

The main two sites that spurred our interest of the group to study this data for our final project is:

 

http://www.ncbi.nlm.nih.gov/bioproject/28331

http://commonfund.nih.gov/hmp/index

 

Other Papers that are referenced in this Project are listed below:

 

"A Database of Phylogenetically Atypical Genes in Archaeal and Bacterial Genomes, Identified Using the DarkHorse Algorithm." BMC Bioinformatics. N.p., n.d. Web. 28 Apr. 2014.

 

Daubin, V., Lerat, E., & Perriere, G. (). The source of laterally transferred genes in bacterial genoms. Genome Biology, 4.

 

"DarkHorse: A Method for Genome-wide Prediction of Horizontal Gene Transfer." Genome Biology. N.p., n.d. Web. 28 Apr. 2014.

 

Dufraigne, C., Fertil, B., Lespinats, S., Giron, A., & Deschavanne, P. (). Detection and characterization of horizontal transfers in prokaryotes using genomic signature.Nucleic Acids Research, 33, e6-e6.

 

Ely, B., & Friedman, R. (). Codon Usage Methods for Horizontal Gene Transfer Detection Generate an Abundance of False Positive and False Negative Results. Current Microbiology, , 639-642.

 

Hayes, W., & Borodovsky, M. (). How to Interpret an Anonymous Bacterial Genome: Machine Learning Approach to Gene Identification. Genome Research, .

 

Hooper, S., & Berg, O. (). Detection of Genes with Atypical Nucleotide Sequence in Microbial Genomes. Journal of Molecular Evolution, , 365-375.

 

Huang, D., Liu, L., Skogerbo, G., Zhang, P., Chen, R., He, S., et al. (). The human microbiome: A hot spot of microbial horizontal gene transfer. Genomics, , 265-270.

 

Neyrolles, O. (). A Benchmark of Parametric Methods for Horizontal Transfers Detection. PLoS ONE, , e9989.