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Volumn 6023 LNCS, Issue , 2010, Pages 228-239

Towards automatic detecting of overlapping genes - Clustered BLAST analysis of viral genomes

Author keywords

BLAST analysis; Clustering; Overlapping genes

Indexed keywords

BIOINFORMATICS; CLUSTER ANALYSIS; GENES; K-MEANS CLUSTERING; MACHINE LEARNING; VIRUSES;

EID: 77952311459     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-12211-8_20     Document Type: Conference Paper
Times cited : (5)

References (42)
  • 1
    • 33646034288 scopus 로고    scopus 로고
    • Gene fusion in Helicobacter pylori: Making the ends meet
    • Sakharkar, K., Sakharkar,M., Chow, V.: Gene fusion in Helicobacter pylori: making the ends meet. Antonie van Leeuwenhoek 89, 169-180 (2006)
    • (2006) Antonie Van Leeuwenhoek , vol.89 , pp. 169-180
    • Sakharkar, K.1    Sakharkar, M.2    Chow, V.3
  • 3
    • 34247884480 scopus 로고    scopus 로고
    • Evolution of gene overlaps: Relative reading frame bias in prokaryotic two-component system genes
    • Cock, P., Whitworth, D.: Evolution of gene overlaps: Relative reading frame bias in prokaryotic two-component system genes. J. Mol. Evol. 64, 457-462 (2007)
    • (2007) J. Mol. Evol. , vol.64 , pp. 457-462
    • Cock, P.1    Whitworth, D.2
  • 4
    • 0033561022 scopus 로고    scopus 로고
    • Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae
    • Fukuda, Y., Washio, T., Tomita, M.: Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. Nucl. Acids Res. 27, 1847-1853 (1999)
    • (1999) Nucl. Acids Res. , vol.27 , pp. 1847-1853
    • Fukuda, Y.1    Washio, T.2    Tomita, M.3
  • 5
    • 0033926304 scopus 로고    scopus 로고
    • Stability and evolution of overlapping genes
    • Krakauer, D.C.: Stability and evolution of overlapping genes. Evolution 54, 731-739 (2000)
    • (2000) Evolution , vol.54 , pp. 731-739
    • Krakauer, D.C.1
  • 6
    • 37849012983 scopus 로고    scopus 로고
    • A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes
    • Lillo, F., Krakauer, D.: A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes. Biol. Direct. 2, 22 (2007)
    • (2007) Biol. Direct. , vol.2 , pp. 22
    • Lillo, F.1    Krakauer, D.2
  • 7
    • 33750156563 scopus 로고    scopus 로고
    • Overlapping genes as rare genomic markers: The phylogeny of γ-Proteobacteria as a case study
    • Luo, Y., Fu, C., Zhang, D.-Y., Lin, K.: Overlapping genes as rare genomic markers: the phylogeny of γ-Proteobacteria as a case study. Trends Genet. 22, 593-596 (2006)
    • (2006) Trends Genet. , vol.22 , pp. 593-596
    • Luo, Y.1    Fu, C.2    Zhang, D.-Y.3    Lin, K.4
  • 8
    • 34547769304 scopus 로고    scopus 로고
    • BPhyOG: An interactive server for genomewide inference of bacterial phylogenies based on overlapping genes
    • Luo, Y., Fu, C., Zhang, D.-Y., Lin, K.: BPhyOG: An interactive server for genomewide inference of bacterial phylogenies based on overlapping genes. BMC Bioinformatics 8, 266 (2007)
    • (2007) BMC Bioinformatics , vol.8 , pp. 266
    • Luo, Y.1    Fu, C.2    Zhang, D.-Y.3    Lin, K.4
  • 9
    • 52649156551 scopus 로고    scopus 로고
    • Same-strand overlapping genes in bacteria: Compositional determinants of phase bias
    • Sabath, N., Graur, D., Landan, G.: Same-strand overlapping genes in bacteria: compositional determinants of phase bias. Biol. Direct. 3, 36 (2008)
    • (2008) Biol. Direct. , vol.3 , pp. 36
    • Sabath, N.1    Graur, D.2    Landan, G.3
  • 10
    • 33947235074 scopus 로고    scopus 로고
    • The Sorcerer II Global Ocean Sampling Expedition: Expanding the universe of protein families
    • (and coworkers)
    • Yooseph, S., Sutton, G., Rusch, D.B. (and coworkers): The Sorcerer II Global Ocean Sampling Expedition: expanding the universe of protein families. PLoS Biol. 5, e16 (2007)
    • (2007) PLoS Biol. , vol.5
    • Yooseph, S.1    Sutton, G.2    Rusch, D.B.3
  • 11
    • 34547577142 scopus 로고    scopus 로고
    • Independent evolution of overlapping polymerase and surface protein genes of hepatitis B virus
    • Zaaijer, H.L., van Hemert, F.J., Koppelman, M.H., Lukashov, V.V.: Independent evolution of overlapping polymerase and surface protein genes of hepatitis B virus. J. Gen. Virol. 88, 2137-2143 (2007)
    • (2007) J. Gen. Virol. , vol.88 , pp. 2137-2143
    • Zaaijer, H.L.1    Van Hemert, F.J.2    Koppelman, M.H.3    Lukashov, V.V.4
  • 12
    • 0031030479 scopus 로고    scopus 로고
    • Constrained evolution with respect to gene overlap of hepatitis B virus
    • Mizokami, M., Orito, E., Ohba, K., Ikeo, K., Lau, J.Y., Gojobori, T.: Constrained evolution with respect to gene overlap of hepatitis B virus. J. Mol. Evol. 44(suppl. 1), 83-90 (1997)
    • (1997) J. Mol. Evol. , vol.44 , Issue.SUPPL. 1 , pp. 83-90
    • Mizokami, M.1    Orito, E.2    Ohba, K.3    Ikeo, K.4    Lau, J.Y.5    Gojobori, T.6
  • 13
    • 55449135271 scopus 로고    scopus 로고
    • Oscillating evolution of a mammalian locus with overlapping reading frames: An XLos/ALEX relay
    • Nekrutenko, A., Wadhawan, S., Goetting-Minesky, P., Makova, K.D.: Oscillating evolution of a mammalian locus with overlapping reading frames: an XLos/ALEX relay. PLoS Genet. 1, 18 (2005)
    • (2005) PLoS Genet. , vol.1 , pp. 18
    • Nekrutenko, A.1    Wadhawan, S.2    Goetting-Minesky, P.3    Makova, K.D.4
  • 15
    • 0036297144 scopus 로고    scopus 로고
    • Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products
    • Guyader, S., Ducray, D.G.: Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J. Gen. Virol. 83, 1799 - 1807 (2002)
    • (2002) J. Gen. Virol. , vol.83 , pp. 1799-1807
    • Guyader, S.1    Ducray, D.G.2
  • 16
    • 0025788445 scopus 로고
    • Diversity of coding strategies in influenza viruses
    • Lamb, R.A., Horvath, C.M.: Diversity of coding strategies in influenza viruses. Trends Genet. 7, 261-266 (1991)
    • (1991) Trends Genet , vol.7 , pp. 261-266
    • Lamb, R.A.1    Horvath, C.M.2
  • 17
    • 33744720139 scopus 로고    scopus 로고
    • Tax and rex: Overlapping genes of the Deltaretrovirus group
    • McGirr, K.M., Buehuring, G.C.: Tax and rex: overlapping genes of the Deltaretrovirus group. Virus Genes 32, 229-239 (2006)
    • (2006) Virus Genes , vol.32 , pp. 229-239
    • McGirr, K.M.1    Buehuring, G.C.2
  • 18
    • 64249128647 scopus 로고    scopus 로고
    • Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses
    • Firth, A.E., Atkins, J.F.: Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses. Virol. J. 6, 32 (2009)
    • (2009) Virol. J. , vol.6 , pp. 32
    • Firth, A.E.1    Atkins, J.F.2
  • 20
    • 58149182726 scopus 로고    scopus 로고
    • EVOG: A database for evolutionary analysis of overlapping genes
    • Kim, D.S., Cho, C.Y., Huh, J.W., Kim, H.S., Cho, H.G.: EVOG: a database for evolutionary analysis of overlapping genes. Nucleic Acids Res. 37, D698-D702 (2009)
    • (2009) Nucleic Acids Res , vol.37
    • Kim, D.S.1    Cho, C.Y.2    Huh, J.W.3    Kim, H.S.4    Cho, H.G.5
  • 21
    • 33750962721 scopus 로고    scopus 로고
    • Frequent appearance of novel protein-coding sequences by frameshift translation
    • Okamura, K., Feuk, L., Marques-Bonet, T., Navarro, A., Scherer, S.W.: Frequent appearance of novel protein-coding sequences by frameshift translation. Genomics 88, 690-697 (2006)
    • (2006) Genomics , vol.88 , pp. 690-697
    • Okamura, K.1    Feuk, L.2    Marques-Bonet, T.3    Navarro, A.4    Scherer, S.W.5
  • 23
    • 38149075952 scopus 로고    scopus 로고
    • Data analysis and bioinformatics
    • Ghosh, A., De, R.K., Pal, S.K. (eds.) PReMI 2007. Springer, Heidelberg
    • Di Ges̀u, V.: Data Analysis and Bioinformatics. In: Ghosh, A., De, R.K., Pal, S.K. (eds.) PReMI 2007. LNCS, vol.4815, pp. 373-388. Springer, Heidelberg (2007)
    • (2007) LNCS , vol.4815 , pp. 373-388
    • Di Ges̀u, V.1
  • 25
    • 77952312785 scopus 로고    scopus 로고
    • National Center for Biotechnology Information (NCBI). NCBI Homepage (2009), http://www.ncbi.nlm.nih.gov/
    • (2009) NCBI Homepage
  • 26
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The european molecular biology open software suite
    • Rice, P., Longden, I., Bleasby, A.: EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16, 276-277 (2000)
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 27
    • 0037756727 scopus 로고    scopus 로고
    • How incorrect annotations evolve - The case of short ORFs
    • Linial, M.: How incorrect annotations evolve - the case of short ORFs. Trends Biotechnol. 21, 298-300 (2003)
    • (2003) Trends Biotechnol , vol.21 , pp. 298-300
    • Linial, M.1
  • 28
    • 77952293904 scopus 로고    scopus 로고
    • National Center for Biotechnology Information (NCBI). The BLAST Databases (2009), ftp://ftp.ncbi.nih.gov/blast/db/
    • (2009) The BLAST Databases
  • 30
  • 31
    • 34548442821 scopus 로고    scopus 로고
    • A general reconfigurable architecture for the BLAST algorithm
    • Sotiriades, E., Dollas, A.: A general reconfigurable architecture for the BLAST algorithm. J. VLSI Signal Process. 48, 189-208 (2007)
    • (2007) J. VLSI Signal Process. , vol.48 , pp. 189-208
    • Sotiriades, E.1    Dollas, A.2
  • 33
    • 34948894065 scopus 로고    scopus 로고
    • The evolution of genome compression and genomic novelty in RNA viruses
    • Belshaw, R., Pybus, O.G.G., Rambaut, A.: The evolution of genome compression and genomic novelty in RNA viruses. Genome Res. 17, 1496-1504 (2007)
    • (2007) Genome Res , vol.17 , pp. 1496-1504
    • Belshaw, R.1    Pybus, O.G.G.2    Rambaut, A.3
  • 34
    • 8744308029 scopus 로고    scopus 로고
    • Properties of overlapping genes are conserved across microbial genomes
    • Johnson, Z.I., Chisholm, S.W.: Properties of overlapping genes are conserved across microbial genomes. Genome Inform. 14, 2268-2272 (2004)
    • (2004) Genome Inform. , vol.14 , pp. 2268-2272
    • Johnson, Z.I.1    Chisholm, S.W.2
  • 35
    • 68849100934 scopus 로고    scopus 로고
    • Two overlapping antiparallel genes encoding the iron regulator DmdR1 and the Adm proteins control siderophore and antibiotic biosynthesis in Streptomyces coelicolor A3(2)
    • Tunca, S., Barreiro, C., Coque, J.J., Martin, J.F.: Two overlapping antiparallel genes encoding the iron regulator DmdR1 and the Adm proteins control siderophore and antibiotic biosynthesis in Streptomyces coelicolor A3(2). FEBS J. 276, 4814-4827 (2009)
    • (2009) FEBS J. , vol.276 , pp. 4814-4827
    • Tunca, S.1    Barreiro, C.2    Coque, J.J.3    Martin, J.F.4
  • 36
    • 33745698561 scopus 로고    scopus 로고
    • Exploring the mycobacteriophage metaproteome: Phage genomics as an educational platform
    • (and coworkers)
    • Hatfull, G.F., Pedulla, M.L., Jacobs-Sera, D. (and coworkers): Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2, e92 (2006)
    • (2006) PLoS Genet. , vol.2
    • Hatfull, G.F.1    Pedulla, M.L.2    Jacobs-Sera, D.3
  • 37
    • 72549101727 scopus 로고    scopus 로고
    • Comparative sequence analysis of A-type inclusion (ATI) and P4c proteins of orthopoxviruses that produce typical and atypical ATI phenotypes
    • Okeke, M.I., Adekoya, O.A., Moens, U., Tryland, M., Traavik, T., Nilssen, O.: Comparative sequence analysis of A-type inclusion (ATI) and P4c proteins of orthopoxviruses that produce typical and atypical ATI phenotypes. Virus Genes 3, 200-209 (2009)
    • (2009) Virus Genes , vol.3 , pp. 200-209
    • Okeke, M.I.1    Adekoya, O.A.2    Moens, U.3    Tryland, M.4    Traavik, T.5    Nilssen, O.6
  • 38
    • 35848952765 scopus 로고    scopus 로고
    • Protein secretion in gram-negative bacteria via the autotransporter pathway
    • Dautin, N., Bernstein, H.D.: Protein secretion in gram-negative bacteria via the autotransporter pathway. Annu. Rev. Microbiol. 61, 89-112 (2007)
    • (2007) Annu. Rev. Microbiol. , vol.61 , pp. 89-112
    • Dautin, N.1    Bernstein, H.D.2
  • 39
    • 33947128217 scopus 로고    scopus 로고
    • Potential evolutionary influences on overlapping reading frames in the bovine leukemia virus pXBL region
    • Zhao, X., McGirr, K.M., Buehring, G.C.: Potential evolutionary influences on overlapping reading frames in the bovine leukemia virus pXBL region. Genomics 89, 502-511 (2007)
    • (2007) Genomics , vol.89 , pp. 502-511
    • Zhao, X.1    McGirr, K.M.2    Buehring, G.C.3
  • 40
    • 68049089607 scopus 로고    scopus 로고
    • PairWise Neighbours database: Overlaps and spacers among prokaryote genomes
    • Palleja, A., Reverter, T., Garcia-Vallve, S., Romeu, A.: PairWise Neighbours database: overlaps and spacers among prokaryote genomes. BMC Genomics 10, 281 (2009)
    • (2009) BMC Genomics , vol.10 , pp. 281
    • Palleja, A.1    Reverter, T.2    Garcia-Vallve, S.3    Romeu, A.4
  • 41
    • 58149492439 scopus 로고    scopus 로고
    • It is computation time for bacteriology
    • Zhulin, I.B.: It is computation time for bacteriology. J. Bacteriol. 191, 20-22 (2009)
    • (2009) J. Bacteriol. , vol.191 , pp. 20-22
    • Zhulin, I.B.1
  • 42
    • 72949101201 scopus 로고    scopus 로고
    • A phylogeny-driven genomic encyclopaedia of bacteria and archaea
    • (coworkers)
    • Wul, D., Hugenholtz, P., Mavromatis, K. (coworkers): A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462, 1056-1060 (2009)
    • (2009) Nature , vol.462 , pp. 1056-1060
    • Wul, D.1    Hugenholtz, P.2    Mavromatis, K.3


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