References

Please feel to free to contact:

• Pierre-Yves Bourguignon name@genopole.cnrs.fr for details on Parcimonious models.
• David Robelin name@genopole.cnrs.fr for details on phased models and statistical calculus.
• Gregory Nuel name@genopole.cnrs.fr for details on Arnoldi algorithms.
• Sophie Lèbre name@genopole.cnrs.fr for details on Mixture Transition Distribution models.

Main reference:

• Miele V, Bourguignon PY, Robelin D, Nuel G, Richard H. (2005) seq++: analyzing biological sequences with a range of Markov-related models. Bioinformatics.

Several references:

• Bourguignon,P.Y., Robelin,D. (2004) Modeles de Markov parcimonieux , Actes de JOBIM.

• Bourguignon,P.Y. (2005)Parcimonious Markov Models, submitted.

• Bühlmann,P., Wyner,A.J. (1999) Variable length Markov chains. Annals of Statistics, 27, 480-513.

• Bulyk M.L., (2003) Computational prediction of transcription-factor binding site locations, Genome Biology, 5:201.

• Borodovsky,M., McIninch,J.D., Koonin,E.V., Rudd,K.E., Medigue,C., Danchin,A., (1995) Detection of new genes in a bacterial genome using Markov models for three gene classes, Nucleic Acids Res., 25, 3554-62.

• Lebre,S. (2004) Estimation de modèle MTD, Evry Univ. Internal Report.

• Lehoucq R.B., Sorensen B., Yang C. (1996) ARPACK user's guide: solution of large-scale eigenvalue problems by implicitly restarted Arnoldi methods. Technical report, Rice University.

• Richard H., Nuel G., (2003) SPA: simple web tool to assess statistical significance of DNA patterns. Nucl. Acids. Res., 31(13):3679-81.

• Robelin D., Richard H., Prum B., (2003) SIC: a tool to detect short inverted segments in a biological sequence. Nucl. Acids. Res., 31(13):3669-71.

• Ron D., Singer Y., Tishby N., (1996) The power of amnesia: learning probabilistic automata with Variable Memory Length, Machine Learning, 25.

• Schbath S., Prum B., Turckheim E. d. (1995) Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comp. Biol., 2:417-437.

• Stormo G.D. (1990) Consensus patterns in DNA. Methods Enzymol., 183:211-221.