Tools for Comparative Genomics

Cite Us

VISTA tools were described in several publications. Please use references relevant to you work. Thank you.

General VISTA references

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004 Jul 1;32 (Web Server issue):W273-9

Dubchak I., Brudno M., Loots G. G., Mayor C., Pachter L., Rubin E. M. and Frazer K. A. (2000) Active Conservation of Noncoding Sequences Revealed by 3-way Species Comparisons. Genome Research, 10:1304.

Visualization program

Mayor C., Brudno M., Schwartz J. R., Poliakov A., Rubin E. M., Frazer K. A., Pachter L. S. and Dubchak I. (2000) VISTA: Visualizing Global DNA Sequence Alignments of Arbitrary Length. Bioinformatics, 16:1046.


O.Couronne, A.Poliakov, N.Bray, T.Ishkhanov, D.Ryaboy, E.Rubin, L.Pachter, I.Dubchak. 2003. Strategies and Tools for Whole-Genome Alignments. Genome Res., 13:7.


Loots, G., Ovcharenko,I., Pachter,L., Dubchak,I., Rubin, E. rVISTA for comparative sequence-based discovery of functional transcription factor binding sites. (2002) Genome. Res. 12:832-839


Shah, N., Couronne, O., Pennacchio, L.A., Brudno, M., Batzoglou, S., Bethel, E.W., Rubin, E.M., Hamann, B. and Dubchak, I., Phylo-VISTA: interactive visualization of DNA multiple alignments. Bioinformatics, to appear.

Whole genome rVISTA

Zambon AC, Zhang L, Minovitsky S, Kanter JR, Prabhakar S, Salomonis N, Vranizan K, Dubchak I, Conklin BR, Insel PA. Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. Proc Natl Acad Sci USA. 2005 Jun 14;102(24):8561-6. Epub 2005 Jun 6.

Alignment programs


Bray, N., Dubchak, I. and Pachter, L. (2003) AVID: A Global Alignment Program. Genome Res., 13:97.


Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., and Batzoglou, S; NISC Comparative Sequencing Program. LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA, 2003. Genome Res., 13(4): 721-731.


Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., and Batzoglou, S. Glocal Alignment: Finding Rearrangements During Alignment, 2003. Bioinformatics, 19S1: i54-i62.