Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome

BMC Genomics

Volumn 4, Issue , 2003, Pages

  Jensen, Lars Juhl ^a   Skovgaard, Marie ^a   Sicheritz Pontén, Thomas ^a   Jørgensen, Merete Kær ^a   Lundegaard, Christiane ^a   Pedersen, Corinna Cavan ^a   Petersen, Nanna ^a   Ussery, David ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; AMINO ACID; ARCHAEAL DNA; ARCHAEAL PROTEIN;

AMINO ACID COMPOSITION; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL GENOME; BINDING SITE; CONTROLLED STUDY; GENE SEQUENCE; GENE TRANSFER; GENETIC CODE; GENOME ANALYSIS; METHANOPYRUS KANDLERI; NONHUMAN; OPEN READING FRAME; PROKARYOTE; PROTEIN LOCALIZATION; SEQUENCE HOMOLOGY; START CODON; THERMOPHILIC BACTERIUM; DNA BASE COMPOSITION; GENE; GENETICS; GENOME; MULTIGENE FAMILY; PHYSIOLOGY; PREDICTION AND FORECASTING; TRANSCRIPTION INITIATION SITE;

ARCHAEA; BACTERIA (MICROORGANISMS); METHANOPYRUS KANDLERI; PROKARYOTA;

AMINO ACIDS; ARCHAEAL PROTEINS; BASE COMPOSITION; DNA, ARCHAEAL; GENES, ARCHAEAL; GENOME, ARCHAEAL; MULTIGENE FAMILY; OPEN READING FRAMES; PREDICTIVE VALUE OF TESTS; TRANSCRIPTION INITIATION SITE;

EID: 9144222217     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-4-12     Document Type: Article

References (36)

1. Skovgaard M, Jensen L, Brunak S, Ussery D and Krogh A On the total number of genes and their length distribution in complete micro-bial geuomes Trends in Genetics 2001, 17: 425-428
2. Rogozin I, Makarova K, Murvai J, Czabarka E, Wolf Y, Tatusov R, Szekely L and Koonin E Connected gene neighborhoods in prokarytic genomes Nucl Acids Res 2002, 30: 2212-2223
3. Slesarev A, Mezhevaya K, Makarova K, Polushin N, Shcherbinina O, Shakhova V, Belova G, Aravind L, Natale D and Rogozin I The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens Proc Natl Acad Sci USA 2002, 99: 4644-4649
4. Sebaihia M, Bentley S, Thomson N, Holden M and Parkhill J Tales of the unexpected Trends in Microbiology 2002, 10: 261-262
5. Jensen L, Friis C and Ussery D Three views of microbial genomes Res Microbiol 1999, 150: 773-777
6. Pedersen A, Jensen L, Stasrfeldt H, Brunak S and Ussery D A DNA structural atlas of E. coli J Mol Biol 2000, 299: 907-930
7. Skovgaard M, Jensen L, Friis C, Stærfeldt HH, Worning P, Brunak S and Ussery D The atlas visualisation of genome-wide information In, Methods in Microbiology (Edited by: Wren B, Dorrell N) Academic Press, London, UK 2002, 33: 49-63
8. Ragan M On surrogate methods for detecting lateral gene transfer FEMS Microbiol Lett 2001, 201: 187-191
9. Hannenhalli S, Hayes W, Hatzigeorgiou A and Fickett J Bacterial start prediction Nucl Acids Res 1999, 27: 3577-3582
10. Besemer J, Lomsadze A and Borodovsky M GeneMarkS: a selftraining method for prediction of gene starts in microbial genomes. implications for finding sequence motifs in regulatory regions Nucl Acids Res 2001, 29: 2607-2618
11. Maidak B, Cole J, Lilburn T, Parker C Jr, Saxman P, Farris R, Garrity G, Olsen G, Schmidt T and Tiedje J The RDP-II (Ribosomal Database Project) Nucl Acids Res 2001, 29: 173-174
12. Gautheret D, Konings D and Gutell R G: U base pairing motifs in ribosomal RNA RNA 1995, 1: 807-814
13. Hafenbradl D, Keller M, Thiericke R and Stetter K A novel unsaturated archaeal ether core lipid from the hyperthermophile Methanopyrus kandleri Syst Appi Microbiol 1993, 16: 165-169
14. Wright P and Dyson H Intrinsically unstructured proteins: Reassessing the protein structure - function paradigm J Mol Biol 1999, 293: 321-331
15. Dunker A and Obradovic Z The protein trinity - linking function and disorder Nature Biotechnology 2001, 19: 805-806
16. Wise M Ojpy: a software tool or low complexity proteins and protein domains Bioinformatics 2001, 17: S288-S295
17. Young I Proof without prejudice: use of the Kolmogorov- Smirnov test for the analysis of histograms from flow systems and other sources J Histochem Cytochem 1977, 25: 935-941
18. Haney P, Badger J, Buldak G, Reich C, Woese C and Olsen G Thermal adaption analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species Proc Nail Acad Sci USA 1999, 96: 3578-3583
19. Kreil D and Ouzounis C Identification of thermophilic species by the amino acid composition deduced from their genomes Nucl Acids Res 2001, 29: 1608-1615
20. Kumar S and Nussinov R How do thermophilic proteins deal with heat? Cell Mol Life Sci 2001, 58: 1216-1233
21. Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Rapp B and Wheeler D GenBank Nucl Acids Res 2002, 30: 17-20
22. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W and Lipman D Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucl Acids Res 1997, 25: 3389-3402
23. Bairoch A and Apweiler R The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 Nucl Acids Res 2000, 28: 45-48
24. Wootton J and Federhen S Statistics of local complexity in amino-acid-sequences and sequence data bases Comput Chem 1993, 17: 149-163
25. Nielsen H, Brunak S and von Heijne G Machine learning approaches for the prediction of signal peptides and other protein sorting signals Protein Eng 1999, 12: 3-9
26. Krogh A, Larsson B, von Heijne G and Sonnhammer E Predicting transmembrane protein topology with a hidden markov model: application to complete genomes J Mol Biol 2001, 305: 567-580
27. Kyte J and Doolittle R A simple method for displaying J Mol Biol 1982, 157: 105-132
28. Guruprasad K, Reddy B and Pandit M Correlation between stability of a protein and its di-peptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence Protein Eng 1990, 4: 155-161
29. Hansen J, Lund O, Tolstrup N, Gooley A, Williams K and Brunak S tOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility Glycoconj J 1998, 15: 115-130
30. Blom N, Gammeltoft S and Brunak S Sequence and structurebased prediction of eukaryotic protein phosphorylation sites J Mol Biol 1999, 294: 1351-1362
31. Rechsteiner M and Rogers S PEST sequences and regulation by pro-teolysis Trends Biochem Sci 1996, 21: 267-271
32. Jones D Protein secondary structure prediction based on position-specific scoring matrices J Mol Biol 1999, 292: 195-202
33. Silverman B Density Estimation for Statistics and Data Analysis Chapman & Hall, London 1986, Chap 3
34. Jensen L and Knudsen S Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation Bioinformatics 2000, 16: 326-333
35. Tamames J, Ouzounis C, Casari G, Sander C and Valencia A EUCLID: automatic classification of proteins in functional classes by their database annotations Bioinformatics 1998, 14: 542-543
36. Andrade M, Brown N, Leroy C, Hoersch S, de Daruvar A, Reich C, Franchini A, Tamames J, Valencia A and Ouzounis C Automated genome sequence analysis and annotation Bioinformatics 1999, 15: 391-412