Homology detection

Henikoff, S., and Henikoff, J. G. (2000). Protein family-based methods for homology detection and analysis. In Bioinformatics, A Practical Approach. (D. Higgins, and W. Taylor, eds.), IRL Press, (In press). 

This chapter anticipates the completion of Arabidopsis thaliana, Drosophila melanogaster, and Homo sapiens genome sequencing projects by reviewing current ideas of the evolution of sequence families. In parallel the related issue of domain homolog detection is discussed in light of continuing efforts to map the complete set of domain families. 

Key words Helicobacter pylori, Proteins, Remote homology detection, Function assignment... 

Many domain families are common to Pfam and PALI, although domain boundaries may not be the same for most of the common families in the two databases. In the case of PALI, domain boundaries are largely determined by three-dimensional structure information. In the case of Pfam, sensitivity of homology detection influences identification of domain boundaries. 

In some proteins, only a part of the H. pylori protein is assigned a functional domain by Pfam and the rest of the protein is not assigned any function. Remote homology detection methods employed in the current analysis have established relationships between these unassigned regions and Pfam domain families. 

Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005 21 951-960. 

The following sections briefly discuss some results and trends in using structure prediction for remote homology detection especially in the genomic context, to aid the structural genomics projects, to further whole genome annotation and to exploit the sequence-to-structure-to-function paradigm for functional predictions. 

Madera, M., and J. Gough. 2002. A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res 30 4312-28. 

Saigo, H., Vert, J.-R, Ueda, N., Akutsu, T. Protein homology detection using string alignment kernels. Bioinformatics 2004,20,1682-9. 

Kuang, R., le, E., Wang, K., Wang, K., Siddiqi, M., Freund, Y., Leslie, C. Profile-based string kernels for remote homology detection and motif extraction. J. Bioinform. Gomput. Biol. 2005, 3,527-50. 

Rangwala, H., Karypis, G. Profile-based direct kernels for remote homology detection and fold recognition. Bioinformatics 2005, 21, 4239 7. 

Hou, Y, Hsu, W, Lee, M.L., Bystroff, C. Efficient remote homology detection using local structure. Bioinformatics 2003,19,2294-301. 

Ben-Hur, A., Brutlag, D. Remote homology detection A motif based approach, in International Conference on Intelligent Systems for Molecular Biology, vol. 11,2003, pp. suppl l 126-33. 

Homology Detection Using String Alignment Kernels. 

---