Abstract
Large-scale studies of the origins and evolution of regulatory mechanisms require quantitative estimates of the abundance and co-occurrence of functional protein domains in the genomes of very diverse organism. Current databases, such as SUPERFAMILY, are not able to provide such quantitative data because of species-specific differences and biases in the existing transcript and protein annotations on which they are based. Here we show that the combination of de novo gene predictors and subsequent HMM-based annotation of SCOP domains in the predicted peptides leads to consistent estimates with acceptable accuracy.
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References
Koonin, E., Aravind, L., Kondrashov, A.: The impact of comparative genomics on our understanding of evolution. Cell 101, 573–576 (2000)
Itoh, M., Nacher, J.C., Kuma, K.i., Goto, S., Kanehisa, M.: Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. Genome Biol. 8, 121 (2007)
Wuchty, S., Almaas, E.: Evolutionary cores of domain co-occurence networks. BMC Evol. Biol. 5, 24 (2005)
Prohaska, S.J., Stadler, P.F., Krakauer, D.C.: Innovation in gene regulation: The case of chromatin computation. J. Theor. Biol. 265, 27–44 (2010)
Murphy, D., Dancis, B., Brown, J.R.: The evolution of core proteins involved in microRNA biogenesis. BMC Evolutionary Biology 8, 92 (2008)
Burge, C., Karlin, S.: Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94 (1997)
Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y.M.B.: Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res. 33, 6494–6506 (2005)
Wilson, D., Pethica, R., Zhou, Y., Talbot, C., Vogel, C., Madera, M., Chothia, C., Gough, J.: SUPERFAMILY — comparative genomics, datamining and sophisticated visualisation. Nucleic Acids Res. 37, D380–D386 (2009)
Bhasi, A., Philip, P., Manikandan, V., Senapathy, P.: ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. Nucleic Acids Res. 37, D703–D711 (2009)
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Parikesit, A.A., Stadler, P.F., Prohaska, S.J. (2010). Detection of Protein Domains in Eukaryotic Genome Sequences. In: Ferreira, C.E., Miyano, S., Stadler, P.F. (eds) Advances in Bioinformatics and Computational Biology. BSB 2010. Lecture Notes in Computer Science(), vol 6268. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15060-9_9
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DOI: https://doi.org/10.1007/978-3-642-15060-9_9
Publisher Name: Springer, Berlin, Heidelberg
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