The manuscript named "WildSpan: mining structured motifs from protein sequences" has been published in Algorithms for Molecular Biology.
A software tool, WildSpan, is developed to discover functional signatures and diagnostic patterns of proteins directly from a set of unaligned protein sequences.
The most distinguishing feature of WildSpan is it link short motifs (local conserved regions) with large flexible gaps to deliver the most frequently observed discontinuous patterns present in related proteins. Though the components of such patterns, named W-patterns here, are largely separated in sequences, they usually form clusters in space and are close to functional regions of proteins. The algorithm WildSpan is eligible in effectively discovering W-patterns without sacrificing mining efficiency. It is demonstrated in this study that the W-patterns discovered by WildSpan provides useful information in several protein-related applications. Moreover, the efficiency of WildSpan executable is desirable for high-throughput annotation in post-genome era.
WildSpan is described in our paper:
Chen-Ming Hsu, Chien-Yu Chen*, and Baw-Jhiune Liu (Mar. 2011) WildSpan: mining structured motifs from protein sequences. Algorithms for Molecular Biology, 6:6. [PubMed]
Darby Tien-Hao Chang, Ting-Ying Chien, Chien-Yu Chen* (Jun. 2009) seeMotif: exploring and visualizing sequence motifs in 3D structures. Nucleic Acids Research, 37(Web Server issue), W552-558.
Ting-Ying Chien, Darby Tien-Hao Chang*, Chien-Yu Chen, Yi-Zhong Weng and Chen-Ming Hsu (Jun. 2008) E1DS: catalytic site prediction based on 1D signatures of concurrent conservation. Nucleic Acids Research, 36(Web Server issue), W291-296.
Chien-Yu Chen, Huai-Kuang Tsai, Chen-Ming Hsu, Mei-Ju May Chen, Hao-Geng Hung, Grace Tzu-Wei Huang, and Wen-Hsiung Li* (Feb. 2008) Discovering gapped binding sites of yeast transcription factors. Proceedings of the National Academy of Sciences of the United States of America, 105(7):2527-2532. [eTFBS Web Site] [PubMed]
Chen-Ming Hsu, Chien-Yu Chen*, Baw-Jhiune Liu, Chih-Chang Huang, Min-Hung Laio, Chien-Chieh Lin and Tzung-Lin Wu (May 2007) Identification of Hot Regions in Protein-Protein Interactions by Sequential Pattern Mining. BMC Bioinformatics,8(Suppl 5):S8.[PubMed]
Chen-Ming Hsu, Chien-Yu Chen*, Baw-Jhiune Liu (Jul. 2006) MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences. Nucleic Acids Res, 34(Web Server issue):W356-W361.[MAGIIC-PRO Web Site] [PubMed]
Chen-Ming Hsu, Chien-Yu Chen*,
Ching-Chi Hsu and Baw-Jhiune Liu (2006) Efficient discovery of
structural motifs from protein sequences with combination of
flexible intra- and inter-block gap constraints. In Proc. of
the 10th Pacific-Asia Conf. on Knowledge Discovery and Data Mining
(PAKDD-06), Sigapore, Springer-Verlag 2006, LNCS 3918:p530-539. [SpringerLink]
Ching Yun University,
Department of Computer Science and Information Engineering,
229, Chien-Hsin Rd., Jung-Li, Taiwan 320, R.O.C.
National Taiwan University,
Department of Bio-Industrial Mechatronics Engineering,
Taipei, 106, Taiwan, R.O.C.
B. J. Liu, Ph. D.,
Yuan Ze University,
Department of Computer Science and Engineering,
135, Yuan-Tung Rd., Jung-Li, Taiwan 320, R.O.C.