Separation of sequences from host-pathogen interface using triplet nucleotide frequencies

Fungal Genetics and Biology

Volumn 44, Issue 4, 2007, Pages 231-241

  Emmersen, Jeppe ^a   Rudd, Stephen ^b   Mewes, Hans Werner ^c   Tetko, Igor V ^c,d  

^a AALBORG UNIVERSITY   (Denmark)

^b TURKU CENTRE FOR BIOTECHNOLOGY   (Finland)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

^d INSTITUTE OF BIOORGANIC CHEMISTRY AND PETROCHEMISTRY   (Ukraine)

Author keywords

Bioinformatics; Codon bias; Codon usage; EST data analysis; Plant fungi interactions

Indexed keywords

ALGORITHM; ARTICLE; FUNGAL VIRULENCE; GENE FREQUENCY; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; HOST PATHOGEN INTERACTION; NONHUMAN; PRIORITY JOURNAL;

ALGORITHMS; CODON; EXPRESSED SEQUENCE TAGS; FUNGI; GENES, FUNGAL; GENES, PLANT; PLANT DISEASES; PLANTS; RNA, FUNGAL; RNA, MESSENGER; RNA, PLANT; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SPECIES SPECIFICITY;

FUNGI;

EID: 33847262505     PISSN: 10871845     EISSN: 10960937     Source Type: Journal    
DOI: 10.1016/j.fgb.2006.11.010     Document Type: Article

References (37)

1. Adams M.D., Soares M.B., Kerlavage A.R., Fields C., and Venter J.C. Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nat. Genet. 4 (1993) 373-380
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
3. Bennet J.W. Fungal genome initiative. Genomics for filamentous fungi. Genet. Biol. 21 (1997) 3-7
4. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., and Wheeler D.L. GenBank. Nucleic Acids Res. 33 (2005) D34-D38
5. Bishop D., and Cooper R.M. An ultrastructural-study of root invasion in three vascular wilt diseases. Physiol. Plant Pathol. (1993) 22
6. Both M., Csukai M., Stumpf M.P., and Spanu P.D. Gene expression profiles of Blumeria graminis indicate dynamic changes to primary metabolism during development of an obligate biotrophic pathogen. Plant Cell 17 (2005) 2107-2122
7. Chang, C.C., Lin, C.J., 2005. LIBSVM: a Library for Support Vector Machines. Available at http://www.csie.ntu.edu.tw/~cjlin/libsvm.
8. Chawla N.V., Bowyer K.W., Hall L.O., and Kegelmeyer W.P. SMOTE: synthetic minority over-sampling technique. J. Artific. Intell. Res. 16 (2002) 321-357
9. Dean R.A., Talbot N.J., Ebbole D.J., Farman M.L., Mitchell T.K., Orbach M.J., Thon M., Kulkarni R., Xu J.R., Pan H., Read N.D., Lee Y.H., Carbone I., Brown D., Oh Y.Y., Donofrio N., Jeong J.S., Soanes D.M., Djonovic S., Kolomiets E., Rehmeyer C., Li W., Harding M., Kim S., Lebrun M.H., Bohnert H., Coughlan S., Butler J., Calvo S., Ma L.J., Nicol R., Purcell S., Nusbaum C., Galagan J.E., and Birren B.W. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434 (2005) 980-986
10. Friedel C.C., Jahn K.H., Sommer S., Rudd S., Mewes H.W., and Tetko I.V. Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage. Bioinformatics 21 (2005) 1383-1388
11. Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D., Jaffe D., FitzHugh W., Ma L.J., Smirnov S., Purcell S., Rehman B., Elkins T., Engels R., Wang S., Nielsen C.B., Butler J., Endrizzi M., Qui D., Ianakiev P., Bell-Pedersen D., Nelson M.A., Werner-Washburne M., Selitrennikoff C.P., Kinsey J.A., Braun E.L., Zelter A., Schulte U., Kothe G.O., Jedd G., Mewes W., Staben C., Marcotte E., Greenberg D., Roy A., Foley K., Naylor J., Stange-Thomann N., Barrett R., Gnerre S., Kamal M., Kamvysselis M., Mauceli E., Bielke C., Rudd S., Frishman D., Krystofova S., Rasmussen C., Metzenberg R.L., Perkins D.D., Kroken S., Cogoni C., Macino G., Catcheside D., Li W., Pratt R.J., Osmani S.A., DeSouza C.P., Glass L., Orbach M.J., Berglund J.A., Voelker R., Yarden O., Plamann M., Seiler S., Dunlap J., Radford A., Aramayo R., Natvig D.O., Alex L.A., Mannhaupt G., Ebbole D.J., Freitag M., Paulsen I., Sachs M.S., Lander E.S., Nusbaum C., and Birren B. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422 (2003) 859-868
12. Gentles A.J., and Karlin S. Genome-scale compositional comparisons in eukaryotes. Genome Res. 11 (2001) 540-546
13. Guldener U., Mannhaupt G., Munsterkotter M., Haase D., Oesterheld M., Stumpflen V., Mewes H.W., and Adam G. FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum. Nucleic Acids Res. 34 (2006) D456-D458
14. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68 (2004) 669-685
15. Hraber P.T., and Weller J.W. On the species of origin: diagnosing the source of symbiotic transcripts. Genome Biol. 2 (2001) RESEARCH0037
16. Huitema E., Torto T.A., Styer A., and Kamoun S. Combined ESTs from plant-microbe interactions: using GC counting to determine the species of origin. Methods Mol. Biol. 236 (2003) 79-84
17. Karlin S. Global dinucleotide signatures and analysis of genomic heterogeneity. Curr. Opin. Microbiol. 1 (1998) 598-610
18. Maor R., Kosman E., Golobinski R., Goodwin P., and Sharon A. PF-IND: probability algorithm and software for separation of plant and fungal sequences. Curr. Genet. 43 (2003) 296-302
19. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., and Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 (2005) 376-380
20. McMullen M., Jones R., and Gallenberg D. Scab of wheat and barley: a re-emerging disease of devastating impact. Plant Dis. 81 (1997) 1340-1348
21. Meyers B.C., Souret F.F., Lu C., and Green P.J. Sweating the small stuff: microRNA discovery in plants. Curr. Opin. Biotechnol. 17 (2006) 1013-1019
22. Miller R.T., Christoffels A.G., Gopalakrishnan C., Burke J., Ptitsyn A.A., Broveak T.R., and Hide W.A. A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res. 9 (1999) 1143-1155
23. Panabieres F., Amselem J., Galiana E., and Le Berre J.Y. Gene identification in the oomycete pathogen Phytophthora parasitica during in vitro vegetative growth through expressed sequence tags. Fungal Genet. Biol. 42 (2005) 611-623
24. Pertea G., Huang X., Liang F., Antonescu V., Sultana R., Karamycheva S., Lee Y., White J., Cheung F., Parvizi B., Tsai J., and Quackenbush J. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19 (2003) 651-652
25. Posada-Buitrago M.L., and Frederick R.D. Expressed sequence tag analysis of the soybean rust pathogen Phakopsora pachyrhizi. Fungal Genet. Biol. 42 (2005) 949-962
26. Quackenbush J., Cho J., Lee D., Liang F., Holt I., Karamycheva S., Parvizi B., Pertea G., Sultana R., and White J. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29 (2001) 159-164
27. Recorbet G., Steinberg C., Olivain C., Edel V., Trouvelot S., Dumas-Gaudot E., Gianinazzi S., and Alabouvette C. Wanted: pathogenesis-related marker molecules for Fusarium oxysporum. New Phytol. 159 (2003) 73-92
28. Rudd S. openSputnik-a database to ESTablish comparative plant genomics using unsaturated sequence collections. Nucleic Acids Res. 33 (2005) D622-D627
29. Rudd S., and Tetko I.V. Eclair-a web service for unravelling species origin of sequences sampled from mixed host interfaces. Nucleic Acids Res. 33 (2005) W724-W727
30. Ruepp A., Zollner A., Maier D., Albermann K., Hani J., Mokrejs M., Tetko I., Guldener U., Mannhaupt G., Munsterkotter M., and Mewes H.W. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32 (2004) 5539-5545
31. Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A., and Shinozaki K. Functional annotation of a full-length Arabidopsis cDNA collection. Science 296 (2002) 141-145
32. Sesma A., and Osbourn A.E. The rice leaf blast pathogen undergoes developmental processes typical of root-infecting fungi. Nature 431 (2004) 582-586
33. Talbot N.J., Ebbole D.J., and Hamer J.E. Identification and characterization of MPG1, a gene involved in pathogenicity from the rice blast fungus Magnaporthe grisea. Plant Cell 5 (1993) 1575-1590
34. Tetko I.V., Bruneau P., Mewes H.W., Rohrer D.C., and Poda G.I. Can we estimate the accuracy of ADME-Tox predictions?. Drug Discov. Today 11 (2006) 700-707
35. Tetko I.V., Solov'ev V.P., Antonov A.V., Yao X., Doucet J.P., Fan B., Hoonakker F., Fourches D., Jost P., Lachiche N., and Varnek A. Benchmarking of linear and nonlinear approaches for quantitative structure-property relationship studies of metal complexation with ionophores. J. Chem. Inf. Model. 46 (2006) 808-819
36. Viaud M.C., Balhadere P.V., and Talbot N.J. A Magnaporthe grisea cyclophilin acts as a virulence determinant during plant infection. Plant Cell 14 (2002) 917-930
37. Yarden O., Ebbole D.J., Freeman S., Rodriguez R.J., and Dickman M.B. Fungal biology and agriculture: revisiting the field. Mol. Plant Microbe Interact. 16 (2003) 859-866