메뉴 건너뛰기




Volumn 5, Issue 1, 2007, Pages 53-58

Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics

Author keywords

annotation; bioinformatics; complete genomes; G language Genome Analysis Environment; software

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BIOINFORMATICS; COMPARATIVE STUDY; COMPUTER PROGRAM; DATA BASE; EMBL NUCLEOTIDE SEQUENCE DATABASE; GENE SEQUENCE; GENOME; GENOME ANALYSIS; GENOMICS; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN LOCALIZATION; SEQUENCE ANALYSIS; VALIDATION PROCESS;

EID: 34250180888     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(07)60014-X     Document Type: Article
Times cited : (4)

References (37)
  • 1
    • 33644520519 scopus 로고    scopus 로고
    • The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
    • Liolios K., et al. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 34 (2006) D332-D334
    • (2006) Nucleic Acids Res. , vol.34
    • Liolios, K.1
  • 3
    • 33846076975 scopus 로고    scopus 로고
    • EMBL Nucleotide Sequence Database in 2006
    • Kulikova T., et al. EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res. 35 (2007) D16-D20
    • (2007) Nucleic Acids Res. , vol.35
    • Kulikova, T.1
  • 4
    • 33846086803 scopus 로고    scopus 로고
    • DDBJ working on evaluation and classification of bacterial genes in INSDC
    • Sugawara H., et al. DDBJ working on evaluation and classification of bacterial genes in INSDC. Nucleic Acids Res. 35 (2007) D13-D15
    • (2007) Nucleic Acids Res. , vol.35
    • Sugawara, H.1
  • 5
    • 0037433717 scopus 로고    scopus 로고
    • Evaluation of annotation strategies using an entire genome sequence
    • Iliopoulos I., et al. Evaluation of annotation strategies using an entire genome sequence. Bioinfor-matics 19 (2003) 717-726
    • (2003) Bioinfor-matics , vol.19 , pp. 717-726
    • Iliopoulos, I.1
  • 6
    • 33748092050 scopus 로고    scopus 로고
    • Genome Reviews: standardizing content and representation of information about complete genomes
    • Sterk P., et al. Genome Reviews: standardizing content and representation of information about complete genomes. Omics 10 (2006) 114-118
    • (2006) Omics , vol.10 , pp. 114-118
    • Sterk, P.1
  • 7
    • 0036175276 scopus 로고    scopus 로고
    • The past, present and future of genome-wide re-annotation
    • COMMENT2001.
    • Ouzounis C.A., and Karp P.O. The past, present and future of genome-wide re-annotation. Genome Biol. 3 (2002) COMMENT2001.
    • (2002) Genome Biol. , vol.3
    • Ouzounis, C.A.1    Karp, P.O.2
  • 8
    • 0035224943 scopus 로고    scopus 로고
    • A functional update of the Escherichia coli K-12 genome
    • RE-SEARCH0035
    • Serres M.H., et al. A functional update of the Escherichia coli K-12 genome. Genome Biol. 2 (2001) RE-SEARCH0035
    • (2001) Genome Biol. , vol.2
    • Serres, M.H.1
  • 9
    • 0035117320 scopus 로고    scopus 로고
    • Genome sequences and great expectations
    • INTERAC-TIONS0001.
    • Iliopoulos I., et al. Genome sequences and great expectations. Genome Biol. 2 (2001) INTERAC-TIONS0001.
    • (2001) Genome Biol. , vol.2
    • Iliopoulos, I.1
  • 10
    • 0036774642 scopus 로고    scopus 로고
    • Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv
    • Camus J.C., et al. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148 (2002) 2967-2973
    • (2002) Microbiology , vol.148 , pp. 2967-2973
    • Camus, J.C.1
  • 11
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt K.D., et al. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35 (2007) D61-D65
    • (2007) Nucleic Acids Res. , vol.35
    • Pruitt, K.D.1
  • 12
    • 0033034745 scopus 로고    scopus 로고
    • Automated genome sequence analysis and annotation
    • Andrade M.A., et al. Automated genome sequence analysis and annotation. Bioinformatics 15 (1999) 391-412
    • (1999) Bioinformatics , vol.15 , pp. 391-412
    • Andrade, M.A.1
  • 13
    • 0030052411 scopus 로고    scopus 로고
    • MAGPIE: automated genome interpretation
    • Gaasterland T., and Sensen C.W. MAGPIE: automated genome interpretation. Trends Genet. 12 (1996) 76-78
    • (1996) Trends Genet. , vol.12 , pp. 76-78
    • Gaasterland, T.1    Sensen, C.W.2
  • 14
    • 33846089658 scopus 로고    scopus 로고
    • PEDANT genome database: 10 years online
    • Riley M.L., et al. PEDANT genome database: 10 years online. Nucleic Acids Res. 35 (2007) D354-D357
    • (2007) Nucleic Acids Res. , vol.35
    • Riley, M.L.1
  • 16
    • 0037561991 scopus 로고    scopus 로고
    • GenDB-an open source genome annotation system for prokaryote genomes
    • Meyer P., et al. GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31 (2003) 2187-2195
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2187-2195
    • Meyer, P.1
  • 17
    • 33745209677 scopus 로고    scopus 로고
    • GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness
    • Arakawa K., et al. GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness. In Silica Biol. 6 (2006) 49-60
    • (2006) In Silica Biol. , vol.6 , pp. 49-60
    • Arakawa, K.1
  • 18
    • 33747863519 scopus 로고    scopus 로고
    • G-language System as a platform for large-scale analysis of high-throughput omics data
    • Arakawa K., and Tomita M. G-language System as a platform for large-scale analysis of high-throughput omics data. J. Pesticide Sci. 31 (2006) 282-288
    • (2006) J. Pesticide Sci. , vol.31 , pp. 282-288
    • Arakawa, K.1    Tomita, M.2
  • 19
    • 0037316319 scopus 로고    scopus 로고
    • G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining
    • Arakawa K., et al. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 19 (2003) 305-306
    • (2003) Bioinformatics , vol.19 , pp. 305-306
    • Arakawa, K.1
  • 20
    • 0032544103 scopus 로고    scopus 로고
    • Self-identification of protein-coding regions in microbial genomes
    • Audic S., and Claverie J.M. Self-identification of protein-coding regions in microbial genomes. Proc. Natl. Acad. Sci. USA 95 (1998) 10026-10031
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 10026-10031
    • Audic, S.1    Claverie, J.M.2
  • 21
    • 0033485517 scopus 로고    scopus 로고
    • Improved microbial gene identification with GLIMMER
    • Delcher A.L., et al. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27 (1999) 4636-4641
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4636-4641
    • Delcher, A.L.1
  • 22
    • 33846041078 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • The UniProt Consortium. The Universal Protein Resource (UniProt). Nucleic Acids Res. 35 (2007) D193-D197
    • (2007) Nucleic Acids Res. , vol.35
    • The UniProt Consortium1
  • 23
    • 0042902833 scopus 로고    scopus 로고
    • The COG database: an updated version includes eukaryotes
    • Tatusov R.L., et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4 (2003) 41
    • (2003) BMC Bioinformatics , vol.4 , pp. 41
    • Tatusov, R.L.1
  • 24
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy S.R. Profile hidden Markov models. Bioinformatics 14 (1998) 755-763
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 25
    • 9144257886 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Bateman A., et al. The Pfam protein families database. Nucleic Acids Res. 32 (2004) D138-D141
    • (2004) Nucleic Acids Res. , vol.32
    • Bateman, A.1
  • 26
    • 15844431346 scopus 로고    scopus 로고
    • PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
    • Gardy J.L., et al. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21 (2005) 617-623
    • (2005) Bioinformatics , vol.21 , pp. 617-623
    • Gardy, J.L.1
  • 27
    • 18644368714 scopus 로고    scopus 로고
    • The Bioperl toolkit: Perl modules for the life sciences
    • Stajich J.E., et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12 (2002) 1611-1618
    • (2002) Genome Res. , vol.12 , pp. 1611-1618
    • Stajich, J.E.1
  • 28
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12 (2002) 656-664
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 29
    • 0034150045 scopus 로고    scopus 로고
    • An automated system for genome analysis to support microbial whole-genome shotgun sequencing
    • Sakiyama T., et al. An automated system for genome analysis to support microbial whole-genome shotgun sequencing. Biosci. Biotechnol. Biochem. 64 (2000) 670-673
    • (2000) Biosci. Biotechnol. Biochem. , vol.64 , pp. 670-673
    • Sakiyama, T.1
  • 30
    • 0034069495 scopus 로고    scopus 로고
    • Gene Ontology: tool for the unification of biology
    • Ashburner M., et al. Gene Ontology: tool for the unification of biology. Nat. Genet. 25 (2000) 25-29
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 31
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul S.F., et al. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 32
    • 0030731108 scopus 로고    scopus 로고
    • The complete genome sequence of the gram-positive bacterium Bacillus subtilis
    • Kunst P., et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390 (1997) 249-256
    • (1997) Nature , vol.390 , pp. 249-256
    • Kunst, P.1
  • 33
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • Blattner F.R., et al. The complete genome sequence of Escherichia coli K-12. Science 277 (1997) 1453-1474
    • (1997) Science , vol.277 , pp. 1453-1474
    • Blattner, F.R.1
  • 34
    • 0028829125 scopus 로고
    • The minimal gene complement of Mycoplasma genitalium
    • Eraser C.M., et al. The minimal gene complement of Mycoplasma genitalium. Science 270 (1995) 397-403
    • (1995) Science , vol.270 , pp. 397-403
    • Eraser, C.M.1
  • 35
    • 0036777599 scopus 로고    scopus 로고
    • Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains
    • Fleischmann R.D., et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacterial. 184 (2002) 5479-5490
    • (2002) J. Bacterial. , vol.184 , pp. 5479-5490
    • Fleischmann, R.D.1
  • 37
    • 11144354360 scopus 로고    scopus 로고
    • Environmental genome shotgun sequencing of the Sargasso Sea
    • Venter J.C., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 (2004) 66-74
    • (2004) Science , vol.304 , pp. 66-74
    • Venter, J.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.