Abstract
Given the amount of sequence data available today, in silico function prediction, which often includes detecting distant evolutionary relationships, requires sophisticated bioinformatic workflows. The algorithms behind these workflows exhibit complex data structures; they need the ability to spawn subtasks and tend to demand large amounts of resources. Performing sequence analytic tasks by manually invoking individual function prediction algorithms having to transform between differing input and output formats has become increasingly obsolete. After a period of linking individual predictors using ad hoc scripts, a number of integrated platforms are finally emerging. We present the ANNOTATOR software environment as an advanced example of such a platform.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., Wheeler, D. L. (2008) GenBank. Nucleic Acids Res 36, D25–D30, 10.1093/nar/gkm929.
Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., et al. (1997) The Complete genome sequence of Escherichia coli K-12. Science 277, 1453–1462, 10.1126/science. 277.5331.1453.
Peña-Castillo, L., Hughes, T. R. (2007) Why are there still over 1000 uncharacterized yeast genes? Genetics 176, 7–14, 10.1534/genetics.107.074468.
Cserzo, M., Eisenhaber, F., Eisenhaber, B., Simon, I. (2004) TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics 20, 136–137.
Tusnády, G. E., Simon, I. (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17, 849–850.
Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305, 567–580, 10.1006/jmbi.2000.4315.
Käll, L., Krogh, A., Sonnhammer, E. L. L. (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338, 1027–1036, 10.1016/j.jmb.2004.03.016.
Schneider, G., Neuberger, G., Wildpaner, M., Tian, S., Berezovsky, I., Eisenhaber, F. (2006) Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. BMC Bioinformatics 7, 164, 10.1186/1471-2105-7-164.
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.
Wootton, J. C. (1994) Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 18, 269–285.
Lupas, A., Van Dyke, M., Stock, J. (1991) Predicting coiled coils from protein sequences. Science 252, 1162–1164, 10.1126/science.252.5009.1162.
Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G. R., Korf, I., Lapp, H., et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12, 1611–1618, 10.1101/gr.361602.
Stajich, J. E. (2007) An Introduction to BioPerl. Methods Mol Biol 406, 535–548.
Mangalam, H. (2002) The Bio* toolkits – a brief overview. Brief Bioinform 3, 296–302.
Rice, P., Longden, I., Bleasby, A. (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16, 276–277.
Misra, S., Crosby, M. A., Mungall, C. J., Matthews, B. B., Campbell, K. S., Hradecky, P., Huang, Y., Kaminker, J. S., Millburn, G. H., Prochnik, S. E., et al. (2002) Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol 3, RESEARCH0083.
Mungall, C. J., Misra, S., Berman, B. P., Carlson, J., Frise, E., Harris, N., Marshall, B., Shu, S., Kaminker, J. S., Prochnik, S. E., et al. (2002) An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol 3, RESEARCH0081.
Meyer, F., Goesmann, A., McHardy, A. C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R., et al. (2003) GenDB – an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31, 2187–2195.
Letondal, C. (2001) A Web interface generator for molecular biology programs in Unix. Bioinformatics 17, 73–82.
Senger, M., Rice, P., Oinn, T. (2003) Soaplab – a unified Sesame door to analysis tools. In Proceedings of the UK e-Science, All Hands Meeting. Simon J Cox, pp. 509–513.
Gudgin, M., Hadley, M., Mendelsohn, N., Jean-Jaques, M., Nielsen, H. (2003) SOAP Version 1.2 Part 1: Messaging Framework. W3C Recommendation. Available at: http://www.w3.org/TR/soap12-part1.
Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M. R., Wipat, A., et al. (2004) Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20, 3045–3054, 10.1093/bioinformatics/bth361.
Wilkinson, M. D., Senger, M., Kawas, E., Bruskiewich, R., Gouzy, J., Noirot, C. (2008) Interoperability with Moby 1.0–It’s better than sharing your toothbrush! Brief Bioinformatics, 10.1093/bib/bbn003, 10.1093/bib/bbn003.
Kawas, E., Senger, M., Wilkinson, M. D. (2006) BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinformatics 7, 523.
Shah, S. P., He, D. Y. M., Sawkins, J. N., Druce, J. C., Quon, G., Lett, D., Zheng, G. X. Y., Xu, T., Ouellette, B. F. F. (2004) Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics 5, 40.
Tang, F., Chua, C. L., Ho, L., Lim, Y. P., Issac, P., Krishnan, A. (2005) Wildfire: distributed, Grid-enabled workflow construction and execution. BMC Bioinformatics 6, 69.
Lian, C. C., Tang, F., Issac, P., Krishnan, A. (2005) GEL: grid execution language. J Parallel Distr Com 65, 857–869.
Eisenhaber, F. (2006) Prediction of protein function. In Discovering Biomolecular Mechanisms with Computational Biology. Springer, US, pp. 39–54.
Promponas, V. J., Enright, A. J., Tsoka, S., Kreil, D. P., Leroy, C., Hamodrakas, S., Sander, C., Ouzounis, C. A. (2000) CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics 16, 915–922.
Wootton, J. C. (1994) Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 18, 269–285.
Dosztányi, Z., Csizmók, V., Tompa, P., Simon, I. (2005) The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 347, 827–839, 10.1016/j.jmb.2005.01.071.
Eisenhaber, B., Bork, P., Eisenhaber, F. (1999) Prediction of potential GPI-modification sites in proprotein sequences. J Mol Biol 292, 741–758, 10.1006/jmbi.1999.3069.
Eisenhaber, B., Wildpaner, M., Schultz, C. J., Borner, G. H. H., Dupree, P., Eisenhaber, F. (2003) Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice. Plant Physiol 133, 1691–1701, 10.1104/pp.103.023580.
Eisenhaber, B., Schneider, G., Wildpaner, M., Eisenhaber, F. (2004) A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe. J Mol Biol 337, 243–253, 10.1016/j.jmb.2004.01.025.
Maurer-Stroh, S., Eisenhaber, B., Eisenhaber, F. (2002) N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J Mol Biol 317, 541–557, 10.1006/jmbi.2002.5426.
Maurer-Stroh, S., Eisenhaber, B., Eisenhaber, F. (2002) N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. J Mol Biol 317, 523–540, 10.1006/jmbi.2002.5425.
Maurer-Stroh, S., Eisenhaber, F. (2005) Refinement and prediction of protein prenylation motifs. Genome Biol 6, R55, 10.1186/gb-2005-6-6-r55.
Neuberger, G., Maurer-Stroh, S., Eisenhaber, B., Hartig, A., Eisenhaber, F. (2003) Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence. J Mol Biol 328, 581–592.
Eddy, S. R. (1998) Profile hidden Markov models. Bioinformatics 14, 755–763.
Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B. A., de Castro, E., Lachaize, C., Langendijk-Genevaux, P. S., Sigrist, C. J. A. (2008) The 20 years of PROSITE. Nucleic Acids Res 36, D245–D249, 10.1093/nar/gkm977.
Schäffer, A. A., Wolf, Y. I., Ponting, C. P., Koonin, E. V., Aravind, L., Altschul, S. F. (1999) IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 15, 1000–1011.
Marchler-Bauer, A., Panchenko, A. R., Shoemaker, B. A., Thiessen, P. A., Geer, L. Y., Bryant, S. H. (2002) CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 30, 281–283.
Letunic, I., Doerks, T., Bork, P. (2009) SMART 6: recent updates and new developments. Nucleic Acids Res 37, D229–D232, 10.1093/nar/gkn808.
Finn, R. D., Tate, J., Mistry, J., Coggill, P. C., Sammut, S. J., Hotz, H., Ceric, G., Forslund, K., Eddy, S. R., Sonnhammer, E. L. L., et al. (2008) The Pfam protein families database. Nucleic Acids Res 36, D281–D288, 10.1093/nar/gkm960.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. (1990) Basic local alignment search tool. J Mol Biol 215, 403–410, 10.1006/jmbi.1990.9999.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Schneider, G., Wildpaner, M., Sirota, F.L., Maurer-Stroh, S., Eisenhaber, B., Eisenhaber, F. (2010). Integrated Tools for Biomolecular Sequence-Based Function Prediction as Exemplified by the ANNOTATOR Software Environment. In: Carugo, O., Eisenhaber, F. (eds) Data Mining Techniques for the Life Sciences. Methods in Molecular Biology, vol 609. Humana Press. https://doi.org/10.1007/978-1-60327-241-4_15
Download citation
DOI: https://doi.org/10.1007/978-1-60327-241-4_15
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60327-240-7
Online ISBN: 978-1-60327-241-4
eBook Packages: Springer Protocols