College of Chemical and Life Sciences

College of Computer, Mathematical and Physical Sciences

Institute for Advanced Computer Studies

Comparative Genomics

CBCB faculty: Steven Salzberg, Art Delcher, Mihaela Pertea, Mihai Pop
CBCB students and staff: Adam Phillippy

Comparing the genomes of two or more related organisms allows us to better understand each of the genomes by concentrating on the similarities and differences between them and correlating these with known biological traits. The regions conserved between the two genomes are likely to have an important function as they were "spared" from the mutations commonly occuring during evolution. Differences between the two genomes, as for example the differences between a pathogen and an antibiotic resistant relative, may shed light upon the mechanism of antibiotic resistance.

The comparative genomics research in our group is focused on the following primary areas:

• Development of efficient tools for genome comparisons - we have developed the MUMmer package, an open-source alignment program specifically designed to allow the comparison of entire genomes or chromosomes at a time.
• Homology based gene prediction - the gene finder TWAIN uses identifiable synteny between regions of the genome sequences of two closely related eukaryotic organisms to refine the gene prediction process.
• Use of comparative genomic information to guide sequence assembly - the AMOScmp program allows the assembly of genomes using a related organism as a reference.
• Identification of differences between pathogen strains that can be used for strain identification - most notably we have identified polymorphisms in Bacillus anthracis that can be used as forensic markers.
• Use of gene cluster conservation to predict operons in completed microbial genomes.

Selected Publications

• Majoros WH, Pertea M, Salzberg SL. Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. Bioinformatics 21(9):1782-1788, 2005.
• M. Pop, A. Phillippy, A.L. Delcher and S.L. Salzberg. Comparative genome assembly. Briefings in Bioinformatics. 5(3), pp. 237-248, 2004.
• S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg. Versatile and open software for comparing large genomes. Genome Biology 5, 2004.
• T.D. Read, S.L.Salzberg, M. Pop, M. Shumway, L. Umayam, L. Jiang, E. Holtzapple, J. Busch, K.L. Smith, J.M. Schupp, D. Solomon, P. Keim, C.M. Fraser. Comparative genome sequencing as a method for discovery of novel polymorphisms in Bacillus anthracis. Science 296, pp. 2028-2033, 2002.
• A.L. Delcher, A. Phillippy, J. Carlton, and S.L. Salzberg. Fast Algorithms for Large-scale Genome Alignment and Comparision. Nucleic Acids Research 30(11), pp. 2478-2483, 2002.
• Jonathan A. Eisen, John F. Heidelberg, Owen White, and Steven L. Salzberg. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1(6), pp. 1-9, 2000.
• A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L. Salzberg. Alignment of Whole Genomes. Nucleic Acids Research, 27(11), pp. 2369-2376, 1999.