메뉴 건너뛰기




Volumn 16, Issue 1, 2015, Pages

MDAT- Aligning multiple domain arrangements

Author keywords

Domain arrangement; Multiple alignment

Indexed keywords

ALIGNMENT; PROTEINS;

EID: 84926154979     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-014-0442-7     Document Type: Article
Times cited : (2)

References (30)
  • 2
    • 77958156358 scopus 로고    scopus 로고
    • How do proteins gain new domains?
    • Marsh JA, Teichmann SA. How do proteins gain new domains?Genome Biol. 2010; 11(7):126.
    • (2010) Genome Biol. , vol.11 , Issue.7 , pp. 126
    • Marsh, J.A.1    Teichmann, S.A.2
  • 3
    • 84860138819 scopus 로고    scopus 로고
    • Evolution of protein domain architectures
    • Forslund K, Sonnhammer ELL. Evolution of protein domain architectures. Methods Mol Biol. 2012; 856:187-216.
    • (2012) Methods Mol Biol. , vol.856 , pp. 187-216
    • Forslund, K.1    Sonnhammer, E.L.L.2
  • 4
    • 84879172714 scopus 로고    scopus 로고
    • Dynamics and adaptive benefits of modular protein evolution
    • Bornberg-Bauer E, Albà M M. Dynamics and adaptive benefits of modular protein evolution. Curr Opin Struct Biol. 2013; 23(3):459-66.
    • (2013) Curr Opin Struct Biol. , vol.23 , Issue.3 , pp. 459-466
    • Bornberg-Bauer, E.1
  • 6
    • 16244423379 scopus 로고    scopus 로고
    • Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions
    • Ekman D, Björklund AK, Frey-Skött J, Elofsson A. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol. 2005; 348(1):231-43.
    • (2005) J Mol Biol. , vol.348 , Issue.1 , pp. 231-243
    • Ekman, D.1    Björklund, A.K.2    Frey-Skött, J.3    Elofsson, A.4
  • 7
    • 67650497792 scopus 로고    scopus 로고
    • Nature of the protein universe
    • Levitt M. Nature of the protein universe. Proc Natl Acad Sci U S A. 2009; 106(27):11079-84.
    • (2009) Proc Natl Acad Sci U S A. , vol.106 , Issue.27 , pp. 11079-11084
    • Levitt, M.1
  • 8
    • 84861434537 scopus 로고    scopus 로고
    • Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution
    • Kersting AR, Bornberg-Bauer E, Moore AD, Grath S. Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. Genome Biol Evol. 2012; 4(3):316-29.
    • (2012) Genome Biol Evol. , vol.4 , Issue.3 , pp. 316-329
    • Kersting, A.R.1    Bornberg-Bauer, E.2    Moore, A.D.3    Grath, S.4
  • 10
    • 84873192706 scopus 로고    scopus 로고
    • Repeated evolution of identical domain architecture in metazoan netrin domain-containing proteins
    • Leclère L, Rentzsch F. Repeated evolution of identical domain architecture in metazoan netrin domain-containing proteins. Genome Biol Evol. 2012; 4(9):883-99.
    • (2012) Genome Biol Evol. , vol.4 , Issue.9 , pp. 883-899
    • Leclère, L.1    Rentzsch, F.2
  • 12
    • 84861139508 scopus 로고    scopus 로고
    • Evolution of the multi-domain structures of virulence genes in the human malaria parasite, Plasmodium falciparum
    • Buckee CO, Recker M. Evolution of the multi-domain structures of virulence genes in the human malaria parasite, Plasmodium falciparum. PLoS Comput Biol. 2012; 8(4):1002451.
    • (2012) PLoS Comput Biol. , vol.8 , Issue.4 , pp. 1002451
    • Buckee, C.O.1    Recker, M.2
  • 13
    • 0348047325 scopus 로고    scopus 로고
    • Structure, diversity, and evolution of protein toxins from spore-forming entomopathogenic bacteria
    • de Maagd RA, Bravo A, Berry C, Crickmore N, Schnepf HE. Structure, diversity, and evolution of protein toxins from spore-forming entomopathogenic bacteria. Annu Rev Genet. 2003; 37:409-33.
    • (2003) Annu Rev Genet. , vol.37 , pp. 409-433
    • de Maagd, R.A.1    Bravo, A.2    Berry, C.3    Crickmore, N.4    Schnepf, H.E.5
  • 14
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: a novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000; 302(2):205-17.
    • (2000) J Mol Biol. , vol.302 , Issue.2 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 15
    • 80054078476 scopus 로고    scopus 로고
    • Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
    • Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 7:539.
    • (2011) Mol Syst Biol. , vol.7 , pp. 539
    • Sievers, F.1    Wilm, A.2    Dineen, D.3    Gibson, T.J.4    Karplus, K.5    Li, W.6
  • 16
    • 84883582879 scopus 로고    scopus 로고
    • DIALIGN at GOBICS-multiple sequence alignment using various sources of external information
    • Ait LA, Yamak Z, Morgenstern B. DIALIGN at GOBICS-multiple sequence alignment using various sources of external information. Nucleic Acids Res. 2013; 41:W3-7.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W3-W7
    • Ait, L.A.1    Yamak, Z.2    Morgenstern, B.3
  • 17
    • 34249857539 scopus 로고    scopus 로고
    • COBALT: constraint-based alignment tool for multiple protein sequences
    • Papadopoulos JS, Agarwala R. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics. 2007; 23(9):1073-79.
    • (2007) Bioinformatics. , vol.23 , Issue.9 , pp. 1073-1079
    • Papadopoulos, J.S.1    Agarwala, R.2
  • 18
    • 84892694478 scopus 로고    scopus 로고
    • Rapid similarity search of proteins using alignments of domain arrangements
    • Terrapon N, Weiner J, Grath S, Moore AD, Bornberg-Bauer E. Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics. 2014; 30(2):274-81.
    • (2014) Bioinformatics. , vol.30 , Issue.2 , pp. 274-281
    • Terrapon, N.1    Weiner, J.2    Grath, S.3    Moore, A.D.4    Bornberg-Bauer, E.5
  • 21
    • 24644457706 scopus 로고    scopus 로고
    • BAliBASE 3.0: latest Developments of the Multiple Sequence Alignment Benchmark
    • Thompson JD, Koehl P, Ripp R, Poch O. BAliBASE 3.0: latest Developments of the Multiple Sequence Alignment Benchmark. Proteins. 2005; 61(1):127-36.
    • (2005) Proteins. , vol.61 , Issue.1 , pp. 127-136
    • Thompson, J.D.1    Koehl, P.2    Ripp, R.3    Poch, O.4
  • 22
    • 0030582739 scopus 로고    scopus 로고
    • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
    • Gotoh O. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol. 1996; 264(4):823-38.
    • (1996) J Mol Biol. , vol.264 , Issue.4 , pp. 823-838
    • Gotoh, O.1
  • 23
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005; 21(7):951-60.
    • (2005) Bioinformatics. , vol.21 , Issue.7 , pp. 951-960
  • 24
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992; 89(22):10915-9.
    • (1992) Proc Natl Acad Sci U S A. , vol.89 , Issue.22 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 27
    • 0024234855 scopus 로고
    • CLUSTAL: a package for performing multiple sequence alignment on a microcomputer
    • Higgins DG, Sharp PM. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1988; 73(1):237-44.
    • (1988) Gene. , vol.73 , Issue.1 , pp. 237-244
    • Higgins, D.G.1    Sharp, P.M.2
  • 28
    • 59549102237 scopus 로고    scopus 로고
    • Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
    • Paten B, Herrero J, Beal K, Birney E. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics. 2008; 25(3):259-91.
    • (2008) Bioinformatics. , vol.25 , Issue.3 , pp. 259-291
    • Paten, B.1    Herrero, J.2    Beal, K.3    Birney, E.4
  • 29
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011; 7(10):1002195.
    • (2011) PLoS Comput Biol. , vol.7 , Issue.10 , pp. 1002195
    • Eddy, S.R.1
  • 30
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005; 33(2):511-8.
    • (2005) Nucleic Acids Res. , vol.33 , Issue.2 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.