Algorithms accessible via Chinook
Chinook is designed to be a dynamically changing environment. This list represents some of the algorithms that we have integrated into it. It is by no means comprehensive or a static list of services that are available
Alignment AlgorithmsCLUSTAL W Thompson JD, Higgins DG, and Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673-80. (*)Conreal Berezikov, E., V. Guryev, R.H. Plasterk, and E. Cuppen. 2004. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res 14: 170-178. DIALIGN 2 B. Morgenstern, K. Frech, A. Dress, and T. Werner. 1998. DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics 14, 1998, 290-294. Lagan and MultiLagan Brudno, M., C.B. Do, G.M. Cooper, M.F. Kim, E. Davydov, E.D. Green, A. Sidow, and S. Batzoglou. 2003. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13: 721-731. Mauve Darling, A., Mau, B., Blattner, F.R., and N. Perna. Mauve. Code available at
http://asap.ahabs.wisc.edu/mauve/index.php (*)Orca Wasserman et al. Unpublished Shuffle-Lagan Brudno, M., S. Malde, A. Poliakov, C.B. Do, O. Couronne, I. Dubchak, and S. Batzoglou. 2003b. Glocal alignment: finding rearrangements during alignment. Bioinformatics 19 Suppl 1: I54-I62. T-Coffee Notredame, C., D.G. Higgins, and J. Heringa. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
Primer PredictionPrimer3 Rosen, S. and H.J. Skaletski. Primer3. Code available at