메뉴 건너뛰기




Volumn 518, Issue 1, 2013, Pages 114-123

GI-POP: A combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects

Author keywords

Genome annotation; Genomic island; Microorganism; Ongoing genome project; Web server

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GENOME ANALYSIS; GENOMIC ISLAND; GI POP; MICROBIAL GENETICS; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; SCIENTIST; SUPPORT VECTOR MACHINE;

EID: 84875374625     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.11.063     Document Type: Article
Times cited : (15)

References (36)
  • 1
    • 33745067721 scopus 로고    scopus 로고
    • Ten years of bacterial genome sequencing: comparative-genomics-based discoveries
    • Binnewies T.T., et al. Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct. Integr. Genomics 2006, 6:165-185.
    • (2006) Funct. Integr. Genomics , vol.6 , pp. 165-185
    • Binnewies, T.T.1
  • 2
    • 0037966260 scopus 로고    scopus 로고
    • Identifying unknown game species: experience with nucleotide sequencing of the mitochondrial cytochrome b gene and a subsequent basic local alignment search tool search
    • Brodmann P.D., Nicholas G., Schaltenbrand P., Ilg E.C. Identifying unknown game species: experience with nucleotide sequencing of the mitochondrial cytochrome b gene and a subsequent basic local alignment search tool search. Eur. Food Res. Technol. 2001, 212:491-496.
    • (2001) Eur. Food Res. Technol. , vol.212 , pp. 491-496
    • Brodmann, P.D.1    Nicholas, G.2    Schaltenbrand, P.3    Ilg, E.C.4
  • 3
    • 79955702502 scopus 로고    scopus 로고
    • LIBSVM: a library for support vector machines
    • (27)
    • Chang C.-C., Lin C.-J. LIBSVM: a library for support vector machines. ACM Trans. Intell. Syst. Technol. 2011, 2(27):1-27. (27).
    • (2011) ACM Trans. Intell. Syst. Technol. , vol.2 , Issue.27 , pp. 1-27
    • Chang, C.-C.1    Lin, C.-J.2
  • 4
    • 43349098495 scopus 로고    scopus 로고
    • Using the Generic Genome Browser (GBrowse)
    • (Chapter 9:Unit 9.9)
    • Donlin M.J. Using the Generic Genome Browser (GBrowse). Curr. Protoc. Bioinformatics 2007, (Chapter 9:Unit 9.9).
    • (2007) Curr. Protoc. Bioinformatics
    • Donlin, M.J.1
  • 6
    • 0033758756 scopus 로고    scopus 로고
    • Pathogenicity islands and the evolution of microbes
    • Hacker J., Kaper J.B. Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 2000, 54:641-679.
    • (2000) Annu. Rev. Microbiol. , vol.54 , pp. 641-679
    • Hacker, J.1    Kaper, J.B.2
  • 7
    • 0025005169 scopus 로고
    • Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia-coli isolates
    • Hacker J., et al. Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia-coli isolates. Microb. Pathog. 1990, 8:213-225.
    • (1990) Microb. Pathog. , vol.8 , pp. 213-225
    • Hacker, J.1
  • 8
    • 0033179042 scopus 로고    scopus 로고
    • Transfer RNAs and pathogenicity islands
    • Hou Y.M. Transfer RNAs and pathogenicity islands. Trends Biochem. Sci. 1999, 24:295-298.
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 295-298
    • Hou, Y.M.1
  • 9
    • 0345237922 scopus 로고    scopus 로고
    • IslandPath: aiding detection of genomic islands in prokaryotes
    • Hsiao W., Wan I., Jones S.J., Brinkman F.S. IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 2003, 19:418-420.
    • (2003) Bioinformatics , vol.19 , pp. 418-420
    • Hsiao, W.1    Wan, I.2    Jones, S.J.3    Brinkman, F.S.4
  • 10
    • 0034780910 scopus 로고    scopus 로고
    • Horizontal gene transfer in prokaryotes: quantification and classification
    • Koonin E.V., Makarova K.S., Aravind L. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 2001, 55:709-742.
    • (2001) Annu. Rev. Microbiol. , vol.55 , pp. 709-742
    • Koonin, E.V.1    Makarova, K.S.2    Aravind, L.3
  • 11
    • 69649109364 scopus 로고    scopus 로고
    • Circos: an information aesthetic for comparative genomics
    • Krzywinski M., et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19:1639-1645.
    • (2009) Genome Res. , vol.19 , pp. 1639-1645
    • Krzywinski, M.1
  • 13
    • 50149094265 scopus 로고    scopus 로고
    • Evaluation of genomic island predictors using a comparative genomics approach
    • Langille M.G.I., Hsiao W.W.L., Brinkman F.S.L. Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 2008, 9.
    • (2008) BMC Bioinformatics , vol.9
    • Langille, M.G.I.1    Hsiao, W.W.L.2    Brinkman, F.S.L.3
  • 15
    • 75549086985 scopus 로고    scopus 로고
    • ACLAME: a classification of mobile genetic elements, update 2010
    • Leplae R., Lima-Mendez G., Toussaint A. ACLAME: a classification of mobile genetic elements, update 2010. Nucleic Acids Res. 2010, 38:D57-D61.
    • (2010) Nucleic Acids Res. , vol.38
    • Leplae, R.1    Lima-Mendez, G.2    Toussaint, A.3
  • 16
    • 0029985398 scopus 로고    scopus 로고
    • Asymmetric substitution patterns in the two DNA strands of bacteria
    • Lobry J.R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 1996, 13:660-665.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 660-665
    • Lobry, J.R.1
  • 17
    • 0029985398 scopus 로고    scopus 로고
    • Asymmetric substitution patterns in the two DNA strands of bacteria
    • Lobry J.R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 1996, 13:660-665.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 660-665
    • Lobry, J.R.1
  • 18
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 19
    • 0347756648 scopus 로고    scopus 로고
    • Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
    • Mantri Y., Williams K.P. Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res. 2004, 32:D55-D58.
    • (2004) Nucleic Acids Res. , vol.32
    • Mantri, Y.1    Williams, K.P.2
  • 20
    • 78651285748 scopus 로고    scopus 로고
    • CDD: a Conserved Domain Database for the functional annotation of proteins
    • Marchler-Bauer A., et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011, 39:D225-D229.
    • (2011) Nucleic Acids Res. , vol.39
    • Marchler-Bauer, A.1
  • 21
    • 2942519433 scopus 로고    scopus 로고
    • SIGI: score-based identification of genomic islands
    • Merkl R. SIGI: score-based identification of genomic islands. BMC Bioinformatics 2004, 5.
    • (2004) BMC Bioinformatics , vol.5
    • Merkl, R.1
  • 22
    • 42449105845 scopus 로고    scopus 로고
    • In silico characterization of proteins: UniProt, InterPro and Integr8
    • Mulder N.J., Kersey P., Pruess M., Apweiler R. In silico characterization of proteins: UniProt, InterPro and Integr8. Mol. Biotechnol. 2008, 38:165-177.
    • (2008) Mol. Biotechnol. , vol.38 , pp. 165-177
    • Mulder, N.J.1    Kersey, P.2    Pruess, M.3    Apweiler, R.4
  • 23
    • 33646804475 scopus 로고    scopus 로고
    • Unsupervised statistical identification of genomic islands using oligonucleotide distributions with application to Vibrio genomes
    • Nag S., Chatterjee R., Chaudhuri K., Chaudhuri P. Unsupervised statistical identification of genomic islands using oligonucleotide distributions with application to Vibrio genomes. Sadhana Acad. Proc. Eng. Sci. 2006, 31:105-115.
    • (2006) Sadhana Acad. Proc. Eng. Sci. , vol.31 , pp. 105-115
    • Nag, S.1    Chatterjee, R.2    Chaudhuri, K.3    Chaudhuri, P.4
  • 24
    • 31544472392 scopus 로고    scopus 로고
    • A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria
    • Ou H.Y., et al. A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res. 2006, 34.
    • (2006) Nucleic Acids Res. , vol.34
    • Ou, H.Y.1
  • 25
    • 0035546223 scopus 로고    scopus 로고
    • Detection of lateral gene transfer among microbial genomes
    • Ragan M.A. Detection of lateral gene transfer among microbial genomes. Curr. Opin. Genet. Dev. 2001, 11:620-626.
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 620-626
    • Ragan, M.A.1
  • 26
    • 35748931450 scopus 로고    scopus 로고
    • Identification of compositionally distinct regions in genomes using the centroid method
    • Rajan I., Aravamuthan S., Mande S.S. Identification of compositionally distinct regions in genomes using the centroid method. Bioinformatics 2007, 23:2672-2677.
    • (2007) Bioinformatics , vol.23 , pp. 2672-2677
    • Rajan, I.1    Aravamuthan, S.2    Mande, S.S.3
  • 27
    • 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. 2000, 16:276-277.
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 28
    • 0032518163 scopus 로고    scopus 로고
    • Microbial gene identification using interpolated Markov models
    • Salzberg S.L., Delcher A.L., Kasif S., White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 1998, 26:544-548.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 544-548
    • Salzberg, S.L.1    Delcher, A.L.2    Kasif, S.3    White, O.4
  • 29
    • 1642475095 scopus 로고    scopus 로고
    • Pathogenicity islands in bacterial pathogenesis
    • Schmidt H., Hensel M. Pathogenicity islands in bacterial pathogenesis. Clin. Microbiol. Rev. 2004, 17:14.
    • (2004) Clin. Microbiol. Rev. , vol.17 , pp. 14
    • Schmidt, H.1    Hensel, M.2
  • 30
    • 0023650543 scopus 로고
    • The Codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp P.M., Li W.H. The Codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987, 15:1281-1295.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 31
    • 63549147824 scopus 로고    scopus 로고
    • DIYA: a bacterial annotation pipeline for any genomics lab
    • Stewart A.C., Osborne B., Read T.D. DIYA: a bacterial annotation pipeline for any genomics lab. Bioinformatics 2009, 25:962-963.
    • (2009) Bioinformatics , vol.25 , pp. 962-963
    • Stewart, A.C.1    Osborne, B.2    Read, T.D.3
  • 32
    • 0033956060 scopus 로고    scopus 로고
    • The COG database: a tool for genome-scale analysis of protein functions and evolution
    • Tatusov R.L., Galperin M.Y., Natale D.A., Koonin E.V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000, 28:33-36.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 33-36
    • Tatusov, R.L.1    Galperin, M.Y.2    Natale, D.A.3    Koonin, E.V.4
  • 33
    • 0035162592 scopus 로고    scopus 로고
    • The COG database: new developments in phylogenetic classification of proteins from complete genomes
    • Tatusov R.L., et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2001, 29:22-28.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 22-28
    • Tatusov, R.L.1
  • 34
    • 0142093984 scopus 로고    scopus 로고
    • Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis
    • Tu Q., Ding D.F. Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis. FEMS Microbiol. Lett. 2003, 221:269-275.
    • (2003) FEMS Microbiol. Lett. , vol.221 , pp. 269-275
    • Tu, Q.1    Ding, D.F.2
  • 36
    • 33846087685 scopus 로고    scopus 로고
    • Towards pathogenomics: a web-based resource for pathogenicity islands
    • Yoon S.H., et al. Towards pathogenomics: a web-based resource for pathogenicity islands. Nucleic Acids Res. 2007, 35:D395-D400.
    • (2007) Nucleic Acids Res. , vol.35
    • Yoon, S.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.