메뉴 건너뛰기




Volumn 12, Issue SUPPL. 1, 2011, Pages

Filtering "genic" open reading frames from genomic DNA samples for advanced annotation

Author keywords

[No Author keywords available]

Indexed keywords

AMPICILLIN; BACTERIAL PROTEIN; BETA LACTAMASE; COMPLEMENTARY DNA; DNA FRAGMENT; DOCKING PROTEIN; GENOMIC DNA; PROTEIN SEC; TRANSACTIVATOR PROTEIN; UNCLASSIFIED DRUG; BACTERIAL DNA;

EID: 79958817089     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-S1-S5     Document Type: Article
Times cited : (18)

References (27)
  • 1
    • 0032560491 scopus 로고    scopus 로고
    • The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis
    • 10.1016/S0014-5793(98)00620-6, 9678589
    • Moszer I. The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis. FEBS Lett 1998, 430(1-2):28-36. 10.1016/S0014-5793(98)00620-6, 9678589.
    • (1998) FEBS Lett , vol.430 , Issue.1-2 , pp. 28-36
    • Moszer, I.1
  • 2
    • 33748714313 scopus 로고    scopus 로고
    • Automated bacterial genome analysis and annotation
    • 10.1016/j.mib.2006.08.002, 16931121
    • Stothard P, Wishart DS. Automated bacterial genome analysis and annotation. Curr Opin Microbiol 2006, 9(5):505-510. 10.1016/j.mib.2006.08.002, 16931121.
    • (2006) Curr Opin Microbiol , vol.9 , Issue.5 , pp. 505-510
    • Stothard, P.1    Wishart, D.S.2
  • 3
    • 34250790725 scopus 로고    scopus 로고
    • Estimating the annotation error rate of curated GO database sequence annotations
    • 10.1186/1471-2105-8-170, 1892569, 17519041
    • Jones CE, Brown AL, Baumann U. Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 2007, 8:170. 10.1186/1471-2105-8-170, 1892569, 17519041.
    • (2007) BMC Bioinformatics , vol.8 , pp. 170
    • Jones, C.E.1    Brown, A.L.2    Baumann, U.3
  • 4
    • 34748833491 scopus 로고    scopus 로고
    • Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach
    • 10.1186/1471-2105-8-284, 1994202, 17683567
    • Andorf C, Dobbs D, Honavar V. Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach. BMC Bioinformatics 2007, 8:284. 10.1186/1471-2105-8-284, 1994202, 17683567.
    • (2007) BMC Bioinformatics , vol.8 , pp. 284
    • Andorf, C.1    Dobbs, D.2    Honavar, V.3
  • 5
    • 78049250483 scopus 로고    scopus 로고
    • More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology
    • 10.1371/journal.pcbi.1000867, 2912341, 20686689
    • Wong WC, Maurer-Stroh S, Eisenhaber F. More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PLoS Comput Biol 2010, 6(7):e1000867. 10.1371/journal.pcbi.1000867, 2912341, 20686689.
    • (2010) PLoS Comput Biol , vol.6 , Issue.7
    • Wong, W.C.1    Maurer-Stroh, S.2    Eisenhaber, F.3
  • 6
    • 52449084495 scopus 로고    scopus 로고
    • Identification and correction of abnormal, incomplete and mispredicted proteins in public databases
    • 10.1186/1471-2105-9-353, 2542381, 18752676
    • Nagy A, Hegyi H, Farkas K, Tordai H, Kozma E, Banyai L, Patthy L. Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. BMC Bioinformatics 2008, 9:353. 10.1186/1471-2105-9-353, 2542381, 18752676.
    • (2008) BMC Bioinformatics , vol.9 , pp. 353
    • Nagy, A.1    Hegyi, H.2    Farkas, K.3    Tordai, H.4    Kozma, E.5    Banyai, L.6    Patthy, L.7
  • 7
    • 7444233131 scopus 로고    scopus 로고
    • ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list
    • 10.1101/gr.2769804, 15489318
    • Brasch MA, Hartley JL, Vidal M. ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list. Genome Res 2004, 14(10B):2001-2009. 10.1101/gr.2769804, 15489318.
    • (2004) Genome Res , vol.14 , Issue.10 B , pp. 2001-2009
    • Brasch, M.A.1    Hartley, J.L.2    Vidal, M.3
  • 8
    • 0037435022 scopus 로고    scopus 로고
    • Protein analysis on a proteomic scale
    • 10.1038/nature01512, 12634794
    • Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale. Nature 2003, 422(6928):208-215. 10.1038/nature01512, 12634794.
    • (2003) Nature , vol.422 , Issue.6928 , pp. 208-215
    • Phizicky, E.1    Bastiaens, P.I.2    Zhu, H.3    Snyder, M.4    Fields, S.5
  • 9
    • 3543070000 scopus 로고    scopus 로고
    • A scaleable and integrated crystallization pipeline applied to mining the Thermotoga maritima proteome
    • DiDonato M, Deacon AM, Klock HE, McMullan D, Lesley SA. A scaleable and integrated crystallization pipeline applied to mining the Thermotoga maritima proteome. J Struct Funct Genomics 2004, 5(1-2):133-146.
    • (2004) J Struct Funct Genomics , vol.5 , Issue.1-2 , pp. 133-146
    • DiDonato, M.1    Deacon, A.M.2    Klock, H.E.3    McMullan, D.4    Lesley, S.A.5
  • 10
    • 0037414465 scopus 로고    scopus 로고
    • Exhaustive enumeration of protein domain families
    • 10.1016/S0022-2836(03)00269-9, 12706730
    • Heger A, Holm L. Exhaustive enumeration of protein domain families. J Mol Biol 2003, 328(3):749-767. 10.1016/S0022-2836(03)00269-9, 12706730.
    • (2003) J Mol Biol , vol.328 , Issue.3 , pp. 749-767
    • Heger, A.1    Holm, L.2
  • 11
    • 76749164479 scopus 로고    scopus 로고
    • Proteome complexity measures based on counting of domain-to-protein links for replicative and non-replicative domains
    • USA: Kluwer Academic Publishers, Kolchanov N, Hofestaedt R, Milanesi L., Norwell MA
    • Kuznetsov V, Pickalov V, Kanapin A, Kolchanov N, Hofestaedt R, Milanesi L. Proteome complexity measures based on counting of domain-to-protein links for replicative and non-replicative domains. Bioinformatics of Genome Regulation and Structure II 2006, 329-341. USA: Kluwer Academic Publishers, Kolchanov N, Hofestaedt R, Milanesi L., Norwell MA.
    • (2006) Bioinformatics of Genome Regulation and Structure II , pp. 329-341
    • Kuznetsov, V.1    Pickalov, V.2    Kanapin, A.3    Kolchanov, N.4    Hofestaedt, R.5    Milanesi, L.6
  • 12
    • 0038104830 scopus 로고    scopus 로고
    • Selecting open reading frames from DNA
    • 10.1101/gr.861503, 430925, 12727911
    • Zacchi P, Sblattero D, Florian F, Marzari R, Bradbury AR. Selecting open reading frames from DNA. Genome Res 2003, 13(5):980-990. 10.1101/gr.861503, 430925, 12727911.
    • (2003) Genome Res , vol.13 , Issue.5 , pp. 980-990
    • Zacchi, P.1    Sblattero, D.2    Florian, F.3    Marzari, R.4    Bradbury, A.R.5
  • 14
    • 21744455909 scopus 로고    scopus 로고
    • Characterizing monoclonal antibody epitopes by filtered gene fragment phage display
    • 1183469, 15720292
    • Di Niro R, Ferrara F, Not T, Bradbury AR, Chirdo F, Marzari R, Sblattero D. Characterizing monoclonal antibody epitopes by filtered gene fragment phage display. Biochem J 2005, 388(Pt 3):889-894. 1183469, 15720292.
    • (2005) Biochem J , vol.388 , Issue.PART 3 , pp. 889-894
    • Di Niro, R.1    Ferrara, F.2    Not, T.3    Bradbury, A.R.4    Chirdo, F.5    Marzari, R.6    Sblattero, D.7
  • 15
    • 0033015460 scopus 로고    scopus 로고
    • Rapid protein-folding assay using green fluorescent protein
    • 10.1038/10904, 10404163
    • Waldo GS, Standish BM, Berendzen J, Terwilliger TC. Rapid protein-folding assay using green fluorescent protein. Nat Biotechnol 1999, 17(7):691-695. 10.1038/10904, 10404163.
    • (1999) Nat Biotechnol , vol.17 , Issue.7 , pp. 691-695
    • Waldo, G.S.1    Standish, B.M.2    Berendzen, J.3    Terwilliger, T.C.4
  • 16
    • 0035130371 scopus 로고    scopus 로고
    • Protein solubility and folding monitored in vivo by structural complementation of a genetic marker protein
    • 10.1038/84389, 11175726
    • Wigley WC, Stidham RD, Smith NM, Hunt JF, Thomas PJ. Protein solubility and folding monitored in vivo by structural complementation of a genetic marker protein. Nat Biotechnol 2001, 19(2):131-136. 10.1038/84389, 11175726.
    • (2001) Nat Biotechnol , vol.19 , Issue.2 , pp. 131-136
    • Wigley, W.C.1    Stidham, R.D.2    Smith, N.M.3    Hunt, J.F.4    Thomas, P.J.5
  • 17
    • 0036933287 scopus 로고    scopus 로고
    • A universal, vector-based system for nucleic acid reading-frame selection
    • 10.1093/protein/15.12.1025, 12601143
    • Lutz S, Fast W, Benkovic SJ. A universal, vector-based system for nucleic acid reading-frame selection. Protein Eng 2002, 15(12):1025-1030. 10.1093/protein/15.12.1025, 12601143.
    • (2002) Protein Eng , vol.15 , Issue.12 , pp. 1025-1030
    • Lutz, S.1    Fast, W.2    Benkovic, S.J.3
  • 19
    • 0032824503 scopus 로고    scopus 로고
    • A simple in vivo assay for increased protein solubility
    • 10.1110/ps.8.9.1908, 2144404, 10493593
    • Maxwell KL, Mittermaier AK, Forman-Kay JD, Davidson AR. A simple in vivo assay for increased protein solubility. Protein Sci 1999, 8(9):1908-1911. 10.1110/ps.8.9.1908, 2144404, 10493593.
    • (1999) Protein Sci , vol.8 , Issue.9 , pp. 1908-1911
    • Maxwell, K.L.1    Mittermaier, A.K.2    Forman-Kay, J.D.3    Davidson, A.R.4
  • 20
    • 77951190947 scopus 로고    scopus 로고
    • A comprehensive analysis of filamentous phage display vectors for cytoplasmic proteins: an analysis with different fluorescent proteins
    • 10.1093/nar/gkp809, 2831335, 19955231
    • Velappan N, Fisher HE, Pesavento E, Chasteen L, D'Angelo S, Kiss C, Longmire M, Pavlik P, Bradbury AR. A comprehensive analysis of filamentous phage display vectors for cytoplasmic proteins: an analysis with different fluorescent proteins. Nucleic Acids Res 2010, 38(4):e22. 10.1093/nar/gkp809, 2831335, 19955231.
    • (2010) Nucleic Acids Res , vol.38 , Issue.4
    • Velappan, N.1    Fisher, H.E.2    Pesavento, E.3    Chasteen, L.4    D'Angelo, S.5    Kiss, C.6    Longmire, M.7    Pavlik, P.8    Bradbury, A.R.9
  • 21
    • 33748595526 scopus 로고    scopus 로고
    • Mechanism-based profiling of enzyme families
    • 10.1021/cr050288g, 16895328
    • Evans MJ, Cravatt BF. Mechanism-based profiling of enzyme families. Chem Rev 2006, 106(8):3279-3301. 10.1021/cr050288g, 16895328.
    • (2006) Chem Rev , vol.106 , Issue.8 , pp. 3279-3301
    • Evans, M.J.1    Cravatt, B.F.2
  • 22
    • 14844283810 scopus 로고    scopus 로고
    • Recombinant protein secretion in Escherichia coli
    • 10.1016/j.biotechadv.2004.11.003, 15763404
    • Mergulhao FJ, Summers DK, Monteiro GA. Recombinant protein secretion in Escherichia coli. Biotechnol Adv 2005, 23(3):177-202. 10.1016/j.biotechadv.2004.11.003, 15763404.
    • (2005) Biotechnol Adv , vol.23 , Issue.3 , pp. 177-202
    • Mergulhao, F.J.1    Summers, D.K.2    Monteiro, G.A.3
  • 23
    • 60849102167 scopus 로고    scopus 로고
    • From cellulosomes to cellulosomics
    • 10.1002/tcr.20160, 19107866
    • Bayer EA, Lamed R, White BA, Flint HJ. From cellulosomes to cellulosomics. Chem Rec 2008, 8(6):364-377. 10.1002/tcr.20160, 19107866.
    • (2008) Chem Rec , vol.8 , Issue.6 , pp. 364-377
    • Bayer, E.A.1    Lamed, R.2    White, B.A.3    Flint, H.J.4
  • 24
    • 34948842866 scopus 로고    scopus 로고
    • Accuracy and quality of massively parallel DNA pyrosequencing
    • 10.1186/gb-2007-8-7-r143, 2323236, 17659080
    • Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8(7):R143. 10.1186/gb-2007-8-7-r143, 2323236, 17659080.
    • (2007) Genome Biol , vol.8 , Issue.7
    • Huse, S.M.1    Huber, J.A.2    Morrison, H.G.3    Sogin, M.L.4    Welch, D.M.5
  • 25
    • 0033015460 scopus 로고    scopus 로고
    • Rapid protein-folding assay using green fluorescent protein
    • 10.1038/10904, 10404163
    • Waldo GS, Standish BM, Berendzen J, Terwilliger TC. Rapid protein-folding assay using green fluorescent protein. Nat Biotechnol 1999, 17(7):691-695. 10.1038/10904, 10404163.
    • (1999) Nat Biotechnol , vol.17 , Issue.7 , pp. 691-695
    • Waldo, G.S.1    Standish, B.M.2    Berendzen, J.3    Terwilliger, T.C.4
  • 26
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    • 10.1093/bioinformatics/bti310, 15728110
    • Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21(9):1859-1875. 10.1093/bioinformatics/bti310, 15728110.
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1859-1875
    • Wu, T.D.1    Watanabe, C.K.2
  • 27
    • 14844294424 scopus 로고    scopus 로고
    • Protein production by auto-induction in high density shaking cultures
    • 10.1016/j.pep.2005.01.016, 15915565
    • Studier FW. Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 2005, 41(1):207-234. 10.1016/j.pep.2005.01.016, 15915565.
    • (2005) Protein Expr Purif , vol.41 , Issue.1 , pp. 207-234
    • Studier, F.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.