Acknowledgements & References

Acknowledgements

本システムは東京大学医科学研究所ゲノム解析センター中井謙太教授の開発されたモチーフ抽出ソフトウェアMelian及びMelinaIIを参考に機能を追加したのものです。 中井先生をはじめMelinaの関係者の方々に感謝いたします。また、本システムで利用しているCONSENSUS、MEME、GIBBS-SAMPLER、MDScanは以下のライセンスに従って利用しております。

License Information

CONSENSUS
MEME
GIBBS-SAMPLER
MDScan

References

[1] Poluliakh, N., Takagi,T. and Nakai, K. (2003) MELINA : motif extraction from promoter regions of potentially co-regulated genes. Bioinformatics 19(3), pp.423-424

[2] Okumura,T., Makiguchi, T., Makita, Y., Yamashita, R. and Nakai, K. (2007) Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions Nucleic Acids Res., 35, W227 - W231.

[3] http://melina2.hgc.jp/

[4] Stormo, G.D. and Hartzell, G.W. (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA, 86, pp.1183-1187

[5] Bailey, T.L. and Elkan, C. (1994) Fitting a mixture model by expection maximization to discover motifs in biopolymers. In Proceedings of 2nd International Conference on Intelligent Systems Molecular Biology. pp.28-36.

[6] Lawrence , C.E., Altschul, S.F., Boguski, M.S., Neuwald, A.F., Liu, J.S. and Wootton, J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, pp.208-214

[7] Liu, X.S., Brutlag, D.L. and Liu, J.S. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation. Nature Biotech, pp.835-839