메뉴 건너뛰기




Volumn 1, Issue 1, 2009, Pages 63-67

The DOE-JGI standard operating procedure for the annotations of microbial genomes

Author keywords

Functional annotation; Gene prediction; Genemark; IMG ER; Joint genome institute; Metagene; Rfam; RNAmmer; TRNA scan

Indexed keywords


EID: 75849124594     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.632     Document Type: Article
Times cited : (184)

References (15)
  • 2
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • PMID:9023104 doi:10.1093/nar/gkm846
    • Lowe TM, Eddy SR. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964 PMID:9023104 doi:10.1093/nar/gkm846
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 3
    • 34250665888 scopus 로고    scopus 로고
    • RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
    • PMID:17452365 doi:10.1093/nar/gkm160
    • Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100-3108 PMID:17452365 doi:10.1093/nar/gkm160
    • (2007) Nucleic Acids Res , vol.35 , pp. 3100-3108
    • Lagesen, K.1    Hallin, P.2    Rodland, E.A.3    Staerfeldt, H.H.4    Rognes, T.5    Ussery, D.W.6
  • 5
    • 65549111754 scopus 로고    scopus 로고
    • Infernal 1.0: Inference of RNA alignments
    • PMID:19307242 doi:10.1093/nar/gki081
    • Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009; 25:1335-1337 PMID:19307242 doi:10.1093/nar/gki081
    • (2009) Bioinformatics , vol.25 , pp. 1335-1337
    • Nawrocki, E.P.1    Kolbe, D.L.2    Eddy, S.R.3
  • 6
    • 34447644810 scopus 로고    scopus 로고
    • CRISPR recognition tool (CRT): A tool for automatic detection of clustered regularly interspaced palindromic repeats
    • PMID:17577412 doi:10.1186/1471-2105-8-209
    • Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 2007; 8:209 PMID:17577412 doi:10.1186/1471-2105-8-209
    • (2007) BMC Bioinformatics , vol.8 , pp. 209
    • Bland, C.1    Ramsey, T.L.2    Sabree, F.3    Lowe, M.4    Brown, K.5    Kyrpides, N.C.6    Hugenholtz, P.7
  • 7
    • 0035875343 scopus 로고    scopus 로고
    • GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    • PMID:11410670
    • Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607-2618 PMID:11410670
    • (2001) Nucleic Acids Res , vol.29 , pp. 2607-2618
    • Besemer, J.1    Lomsadze, A.2    Borodovsky, M.3
  • 8
    • 84860915862 scopus 로고    scopus 로고
    • Anonymous. PILER Genomic repeat analysis software
    • Anonymous. PILER Genomic repeat analysis software. 2009 http://www.drive5.com/pilercr
    • (2009)
  • 9
    • 33750976398 scopus 로고    scopus 로고
    • MetaGene: Prokaryotic gene finding from environmental genome shotgun sequences
    • PMID:17028096 doi: 10.1093/nar/gkl723
    • Noguchi H, Park J, Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res 2006; 34:5623-5630 PMID:17028096 doi: 10.1093/nar/gkl723
    • (2006) Nucleic Acids Res , vol.34 , pp. 5623-5630
    • Noguchi, H.1    Park, J.2    Takagi, T.3
  • 13
    • 0037249633 scopus 로고    scopus 로고
    • The TIGRFAMs database of protein families
    • PMID:12520025
    • Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res 2003; 31:371-373 PMID:12520025
    • (2003) Nucleic Acids Res , vol.31 , pp. 371-373
    • Haft, D.H.1    Selengut, J.D.2    White, O.3
  • 14
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • PMID: 9918945
    • Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14:755-763 PMID: 9918945
    • (1998) Bioin Formatics , vol.14 , pp. 755-763
    • Eddy, S.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.