Protein homology detection by HMM--HMM comparison
作者： J. Soding
DOI: 10.1093/BIOINFORMATICS/BTI125
关键词:
摘要: … Here, we generalize the log-odds score maximized in HMM–sequence alignment to the case of HMM–HMM alignment. We present a novel algorithm for HMM–HMM alignment that is …
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S Pietrokovski, Searching databases of conserved sequence regions by aligning protein multiple-alignments Nucleic Acids Research. ,vol. 24, pp. 3836- 3845 ,(1996) , 10.1093/NAR/24.19.3836
Jeanette Hargbo, Arne Elofsson, Hidden Markov models that use predicted secondary structures for fold recognition. Proteins. ,vol. 36, pp. 68- 76 ,(1999) , 10.1002/(SICI)1097-0134(19990701)36:1<68::AID-PROT6>3.0.CO;2-1
Steven Henikoff, Jorja G. Henikoff, Position-based sequence weights☆ Journal of Molecular Biology. ,vol. 243, pp. 574- 578 ,(1994) , 10.1016/0022-2836(94)90032-9
Christopher L. Tang, Lei Xie, Ingrid Y.Y. Koh, Shoshana Posy, Emil Alexov, Barry Honig, On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. Journal of Molecular Biology. ,vol. 334, pp. 1043- 1062 ,(2003) , 10.1016/J.JMB.2003.10.025
G. Gonnet, M. Cohen, S. Benner, Exhaustive matching of the entire protein sequence database Science. ,vol. 256, pp. 1443- 1445 ,(1992) , 10.1126/SCIENCE.1604319
R. Doolittle, Similar Amino Acid Sequences: Chance or Common Ancestry? Science. ,vol. 214, pp. 149- 159 ,(1981) , 10.1126/SCIENCE.7280687
Wolfgang Kabsch, Christian Sander, None, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers. ,vol. 22, pp. 2577- 2637 ,(1983) , 10.1002/BIP.360221211
Kevin Karplus, Rachel Karchin, Christian Barrett, Spencer Tu, Melissa Cline, Mark Diekhans, Leslie Grate, Jonathan Casper, Richard Hughey, What is the value added by human intervention in protein structure prediction Proteins. ,vol. 45, pp. 86- 91 ,(2001) , 10.1002/PROT.10021
Sean R Eddy, None, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids ,(1998)
W. R. Pearson, D. J. Lipman, Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 85, pp. 2444- 2448 ,(1988) , 10.1073/PNAS.85.8.2444