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Volumn 6, Issue 4, 2016, Pages

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

Author keywords

B30.2; Gene conversion; Genome evolution; Innate immune system; NACHT; SPRY

Indexed keywords

NUCLEOTIDE BINDING OLIGOMERIZATION DOMAIN LIKE RECEPTOR; ZEBRAFISH PROTEIN;

EID: 84978866139     PISSN: None     EISSN: 20462441     Source Type: Journal    
DOI: 10.1098/rsob.160009     Document Type: Article
Times cited : (100)

References (62)
  • 1
    • 0034194079 scopus 로고    scopus 로고
    • The NACHT family - A new group of predicted NTPases implicated in apoptosis and MHC transcription activation
    • Koonin EV, Aravind L. 2000 The NACHT family - a new group of predicted NTPases implicated in apoptosis and MHC transcription activation. Trends Biochem. Sci. 25, 223-224. (doi:10.1016/S0968- 0004(00)01577-2)
    • (2000) Trends Biochem. Sci , vol.25 , pp. 223-224
    • Koonin, E.V.1    Aravind, L.2
  • 2
    • 44349171085 scopus 로고    scopus 로고
    • The Nod-like receptor (nlr) family: A tale of similarities and differences
    • Proell M, Riedl SJ, Fritz JH, Rojas AM, Schwarzenbacher R. 2008 The Nod-like receptor (nlr) family: a tale of similarities and differences. PLoS ONE 3, e2119. (doi:10.1371/journal.pone. 0002119)
    • (2008) PLoS ONE , vol.3
    • Proell, M.1    Riedl, S.J.2    Fritz, J.H.3    Rojas, A.M.4    Schwarzenbacher, R.5
  • 3
    • 40449140937 scopus 로고    scopus 로고
    • The NLR gene family: A standard nomenclature
    • Ting JPY et al. 2008 The NLR gene family: a standard nomenclature. Immunity 28, 285-287. (doi:10.1016/j.immuni.2008.02.005)
    • (2008) Immunity , vol.28 , pp. 285-287
    • Ting, J.P.Y.1
  • 4
    • 28444459897 scopus 로고    scopus 로고
    • How Toll-like receptors and Nod-like receptors contribute to innate immunity in mammals
    • Fritz JH, Girardin SE. 2005 How Toll-like receptors and Nod-like receptors contribute to innate immunity in mammals. J. Endotoxin Res. 11, 390-394. (doi:10.1177/09680519050110060301)
    • (2005) J. Endotoxin Res , vol.11 , pp. 390-394
    • Fritz, J.H.1    Girardin, S.E.2
  • 5
    • 33745847180 scopus 로고    scopus 로고
    • TLRs, NLRs and RLRs: A trinity of pathogen sensors that co-operate in innate immunity
    • Creagh EM, O'Neill LAJ. 2006 TLRs, NLRs and RLRs: a trinity of pathogen sensors that co-operate in innate immunity. Trends Immunol. 27, 352-357. (doi:10.1016/j.it.2006.06.003)
    • (2006) Trends Immunol , vol.27 , pp. 352-357
    • Creagh, E.M.1    O'Neill, L.A.J.2
  • 6
    • 33845456631 scopus 로고    scopus 로고
    • Triggering receptor expressed on myeloid cells-1 (TREM-1) amplifies the signals induced by the NACHT-LRR (NLR) pattern recognition receptors
    • Netea MG, Azam T, Ferwerda G, Girardin SE, Kim SH, Dinarello CA. 2006 Triggering receptor expressed on myeloid cells-1 (TREM-1) amplifies the signals induced by the NACHT-LRR (NLR) pattern recognition receptors. J. Leukoc. Biol. 80, 1454-1461. (doi:10.1189/jlb.1205758)
    • (2006) J. Leukoc. Biol , vol.80 , pp. 1454-1461
    • Netea, M.G.1    Azam, T.2    Ferwerda, G.3    Girardin, S.E.4    Kim, S.H.5    Dinarello, C.A.6
  • 7
    • 42149124615 scopus 로고    scopus 로고
    • Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish
    • Stein C, Caccamo M, Laird G, Leptin M. 2007 Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish. Genome Biol. 8, R251. (doi:10. 1186/gb-2007-8-11-r251)
    • (2007) Genome Biol , vol.8 , pp. R251
    • Stein, C.1    Caccamo, M.2    Laird, G.3    Leptin, M.4
  • 8
    • 78751620798 scopus 로고    scopus 로고
    • NLR functions beyond pathogen recognition
    • Kufer TA, Sansonetti PJ. 2011 NLR functions beyond pathogen recognition. Nat. Immunol. 12, 121-128. (doi:10.1038/ni.1985)
    • (2011) Nat. Immunol , vol.12 , pp. 121-128
    • Kufer, T.A.1    Sansonetti, P.J.2
  • 9
    • 84857062410 scopus 로고    scopus 로고
    • A new eye on NLR proteins: Focused on clarity or diffused by complexity
    • Bonardi V, Cherkis K, Nishimura MT, Dangl JL. 2012 A new eye on NLR proteins: focused on clarity or diffused by complexity? Curr. Opin. Immunol. 24, 41-50. (doi:10.1016/j.coi.2011.12.006)
    • (2012) Curr. Opin. Immunol , vol.24 , pp. 41-50
    • Bonardi, V.1    Cherkis, K.2    Nishimura, M.T.3    Dangl, J.L.4
  • 10
    • 84879254416 scopus 로고    scopus 로고
    • Lineagespecific expansion of IFIT gene family: An insight into coevolution with IFN gene family
    • Liu Y, Zhang Y-B, Liu T-K, Gui J-F. 2013 Lineagespecific expansion of IFIT gene family: an insight into coevolution with IFN gene family. PLoS ONE 8, e66859. (doi:10.1371/journal.pone. 0066859)
    • (2013) PLoS ONE , vol.8
    • Liu, Y.1    Zhang, Y.-B.2    Liu, T.-K.3    Gui, J.-F.4
  • 11
    • 84900469574 scopus 로고    scopus 로고
    • Zebrafish as a model for zoonotic aquatic pathogens
    • Rowe HM, Withey JH, Neely MN. 2014 Zebrafish as a model for zoonotic aquatic pathogens. Dev. Comp. Immunol. 46, 96-107. (doi:10.1016/j.dci.2014. 02.014)
    • (2014) Dev. Comp. Immunol , vol.46 , pp. 96-107
    • Rowe, H.M.1    Withey, J.H.2    Neely, M.N.3
  • 12
    • 84900509473 scopus 로고    scopus 로고
    • Studying the immune response to human viral infections using zebrafish
    • Goody MF, Sullivan C, Kim CH. 2014 Studying the immune response to human viral infections using zebrafish. Dev. Comp. Immunol. 46, 84-95. (doi:10. 1016/j.dci.2014.03.025)
    • (2014) Dev. Comp. Immunol , vol.46 , pp. 84-95
    • Goody, M.F.1    Sullivan, C.2    Kim, C.H.3
  • 13
    • 40949159815 scopus 로고    scopus 로고
    • A genomic view of the NOD-like receptor family in teleost fish: Identification of a novel NLR subfamily in zebrafish
    • Laing KJ, Purcell MK, Winton JR, Hansen JD. 2008 A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish. BMC Evol. Biol. 8, 42. (doi:10.1186/ 1471-2148-8-42)
    • (2008) BMC Evol. Biol , vol.8 , pp. 42
    • Laing, K.J.1    Purcell, M.K.2    Winton, J.R.3    Hansen, J.D.4
  • 15
    • 0030920610 scopus 로고    scopus 로고
    • Sequence mapping by electronic PCR
    • Schuler GD. 1997 Sequence mapping by electronic PCR. Genome Res. 7, 541-550.
    • (1997) Genome Res , vol.7 , pp. 541-550
    • Schuler, G.D.1
  • 16
    • 84876043102 scopus 로고    scopus 로고
    • Lamprey immunity is far from primitive
    • Rast JP, Buckley KM. 2013 Lamprey immunity is far from primitive. Proc. Natl Acad. Sci. USA 110, 5746-5747. (doi:10.1073/pnas.1303541110)
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 5746-5747
    • Rast, J.P.1    Buckley, K.M.2
  • 17
    • 84891816495 scopus 로고    scopus 로고
    • The characterization of sponge NLRs provides insight into the origin and evolution of this innate immune gene family in animals
    • Yuen B, Bayes JM, Degnan SM. 2014 The characterization of sponge NLRs provides insight into the origin and evolution of this innate immune gene family in animals. Mol. Biol. Evol. 31, 106-120. (doi:10.1093/molbev/mst174)
    • (2014) Mol. Biol. Evol , vol.31 , pp. 106-120
    • Yuen, B.1    Bayes, J.M.2    Degnan, S.M.3
  • 18
    • 33846808910 scopus 로고    scopus 로고
    • RTK and TGF-b signaling pathways genes in the sea urchin genome
    • Lapraz F et al. 2006 RTK and TGF-b signaling pathways genes in the sea urchin genome. Dev. Biol. 300, 132-152. (doi:10.1016/j.ydbio. 2006.08.048)
    • (2006) Dev. Biol , vol.300 , pp. 132-152
    • Lapraz, F.1
  • 19
    • 84945498007 scopus 로고    scopus 로고
    • Using optical mapping data for the improvement of vertebrate genome assemblies
    • Howe K, Wood JM. 2015 Using optical mapping data for the improvement of vertebrate genome assemblies. Gigascience 4, 10. (doi:10.1186/s13742- 015-0052-y)
    • (2015) Gigascience , vol.4 , pp. 10
    • Howe, K.1    Wood, J.M.2
  • 20
    • 0035544490 scopus 로고    scopus 로고
    • Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): An overview
    • Sola L, Gornung E. 2001 Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview. Genetica 111, 397-412. (doi:10.1023/A:1013776323077)
    • (2001) Genetica , vol.111 , pp. 397-412
    • Sola, L.1    Gornung, E.2
  • 22
    • 84904267838 scopus 로고    scopus 로고
    • The NLR-related protein NWD1 is associated with prostate cancer and modulates androgen receptor signaling
    • Correa RG, Krajewska M, Ware CF, Gerlic M, Reed JC. 2014 The NLR-related protein NWD1 is associated with prostate cancer and modulates androgen receptor signaling. Oncotarget 5, 1666-1682. (doi:10.18632/oncotarget.1850)
    • (2014) Oncotarget , vol.5 , pp. 1666-1682
    • Correa, R.G.1    Krajewska, M.2    Ware, C.F.3    Gerlic, M.4    Reed, J.C.5
  • 23
    • 46449138598 scopus 로고    scopus 로고
    • Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity
    • Huang S et al. 2008 Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity. Genome Res. 18, 1112-1126. (doi:10.1101/gr. 069674.107)
    • (2008) Genome Res , vol.18 , pp. 1112-1126
    • Huang, S.1
  • 24
    • 0345107239 scopus 로고    scopus 로고
    • Selection in the evolution of gene duplications
    • Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. 2002 Selection in the evolution of gene duplications. Genome Biol. 3, research0008.1. (doi:10.1186/gb- 2002-3-2-research0008)
    • (2002) Genome Biol , vol.3
    • Kondrashov, F.A.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 25
    • 84869130037 scopus 로고    scopus 로고
    • Gene duplication as a mechanism of genomic adaptation to a changing environment
    • Kondrashov FA. 2012 Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc. R. Soc. B 279, 5048-5057. (doi:10.1098/rspb.2012.1108)
    • (2012) Proc. R. Soc. B , vol.279 , pp. 5048-5057
    • Kondrashov, F.A.1
  • 26
    • 51349160670 scopus 로고    scopus 로고
    • Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish
    • Chen Z et al. 2008 Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish. Proc. Natl Acad. Sci. USA 105, 12944-12949. (doi:10.1073/pnas.0802432105)
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 12944-12949
    • Chen, Z.1
  • 28
    • 84871832159 scopus 로고    scopus 로고
    • The complex NOD-like receptor repertoire of the coral Acropora digitifera includes novel domain combinations
    • Hamada M, Shoguchi E, Shinzato C, Kawashima T, Miller DJ, Satoh N. 2012 The complex NOD-like receptor repertoire of the coral Acropora digitifera includes novel domain combinations. Mol. Biol. Evol. 30, 167-176. (doi:10.1093/molbev/mss213)
    • (2012) Mol. Biol. Evol , vol.30 , pp. 167-176
    • Hamada, M.1    Shoguchi, E.2    Shinzato, C.3    Kawashima, T.4    Miller, D.J.5    Satoh, N.6
  • 29
    • 51649097483 scopus 로고    scopus 로고
    • Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties
    • Sardiello M, Cairo S, Fontanella B, Ballabio A, Meroni G. 2008 Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties. BMC Evol. Biol. 8, 225. (doi:10.1186/1471-2148-8-225)
    • (2008) BMC Evol. Biol , vol.8 , pp. 225
    • Sardiello, M.1    Cairo, S.2    Fontanella, B.3    Ballabio, A.4    Meroni, G.5
  • 30
    • 33644696909 scopus 로고    scopus 로고
    • Germline and somatic diversification of immune recognition elements in metazoa
    • Pasquier LD. 2006 Germline and somatic diversification of immune recognition elements in metazoa. Immunol. Lett. 104, 2-17. (doi:10.1016/j. imlet.2005.11.022)
    • (2006) Immunol. Lett , vol.104 , pp. 2-17
    • Pasquier, L.D.1
  • 31
    • 0024315266 scopus 로고
    • Gene conversion and the generation of antibody diversity
    • Wysocki LJ, Gefter ML. 1989 Gene conversion and the generation of antibody diversity. Annu. Rev. Biochem. 58, 509-531. (doi:10.1146/annurev.bi. 58.070189.002453)
    • (1989) Annu. Rev. Biochem , vol.58 , pp. 509-531
    • Wysocki, L.J.1    Gefter, M.L.2
  • 32
  • 33
    • 0022977037 scopus 로고
    • Gene correction in the evolution of the T cell receptor beta chain
    • Jouvin-Marche E, Heller M, Rudikoff S. 1986 Gene correction in the evolution of the T cell receptor beta chain. J. Exp. Med. 164, 2083-2088. (doi:10. 1084/jem.164.6.2083)
    • (1986) J. Exp. Med , vol.164 , pp. 2083-2088
    • Jouvin-Marche, E.1    Heller, M.2    Rudikoff, S.3
  • 34
    • 33845663050 scopus 로고    scopus 로고
    • Structural basis for protein recognition by B30.2/SPRY domains
    • Woo J-S, Suh H-Y, Park S-Y, Oh B-H. 2006 Structural basis for protein recognition by B30.2/SPRY domains. Mol. Cell 24, 967-976. (doi:10.1016/j. molcel.2006.11.009)
    • (2006) Mol. Cell , vol.24 , pp. 967-976
    • Woo, J.-S.1    Suh, H.-Y.2    Park, S.-Y.3    Oh, B.-H.4
  • 35
    • 70349997549 scopus 로고    scopus 로고
    • Population genetic models of duplicated genes
    • Innan H. 2009 Population genetic models of duplicated genes. Genetica 137, 19-37. (doi:10. 1007/s10709-009-9355-1)
    • (2009) Genetica , vol.137 , pp. 19-37
    • Innan, H.1
  • 36
    • 1942485886 scopus 로고    scopus 로고
    • The effect of gene conversion on the divergence between duplicated genes
    • Teshima KM, Innan H. 2004 The effect of gene conversion on the divergence between duplicated genes. Genetics 166, 1553-1560. (doi:10.1534/ genetics.166.3.1553)
    • (2004) Genetics , vol.166 , pp. 1553-1560
    • Teshima, K.M.1    Innan, H.2
  • 37
    • 1542288934 scopus 로고    scopus 로고
    • The cytoplasmic body component TRIM5a restricts HIV-1 infection in old world monkeys
    • Stremlau M, Owens CM, Perron MJ, Kiessling M, Autissier P, Sodroski J. 2004 The cytoplasmic body component TRIM5a restricts HIV-1 infection in old world monkeys. Nature 427, 848-853. (doi:10. 1038/nature02343)
    • (2004) Nature , vol.427 , pp. 848-853
    • Stremlau, M.1    Owens, C.M.2    Perron, M.J.3    Kiessling, M.4    Autissier, P.5    Sodroski, J.6
  • 38
    • 17644366913 scopus 로고    scopus 로고
    • NOD-LRR proteins: Role in host-microbial interactions and inflammatory disease
    • Inohara N, Chamaillard M, McDonald C, Nunez G. 2005 NOD-LRR proteins: role in host-microbial interactions and inflammatory disease. Annu. Rev. Biochem. 74, 355-383. (doi:10.1146/annurev. biochem.74.082803.133347)
    • (2005) Annu. Rev. Biochem , vol.74 , pp. 355-383
    • Inohara, N.1    Chamaillard, M.2    McDonald, C.3    Nunez, G.4
  • 39
    • 32944464648 scopus 로고    scopus 로고
    • Pathogen recognition and innate immunity
    • Akira S, Uematsu S, Takeuchi O. 2006 Pathogen recognition and innate immunity. Cell 124, 783-801. (doi:10.1016/j.cell.2006.02.015)
    • (2006) Cell , vol.124 , pp. 783-801
    • Akira, S.1    Uematsu, S.2    Takeuchi, O.3
  • 40
    • 63649108380 scopus 로고    scopus 로고
    • The roles of TLRs, RLRs and NLRs in pathogen recognition
    • Kawai T, Akira S. 2009 The roles of TLRs, RLRs and NLRs in pathogen recognition. Int. Immunol. 21, 317-337. (doi:10.1093/intimm/dxp017)
    • (2009) Int. Immunol , vol.21 , pp. 317-337
    • Kawai, T.1    Akira, S.2
  • 41
    • 0041694469 scopus 로고    scopus 로고
    • Development and maturation of the immune system in zebrafish, Danio rerio: A gene expression profiling, in situ hybridization and immunological study
    • Lam SH, Chua HL, Gong Z, Lam TJ, Sin YM. 2004 Development and maturation of the immune system in zebrafish, Danio rerio: a gene expression profiling, in situ hybridization and immunological study. Dev. Comp. Immunol. 28, 9-28. (doi:10. 1016/S0145-305X(03)00103-4)
    • (2004) Dev. Comp. Immunol , vol.28 , pp. 9-28
    • Lam, S.H.1    Chua, H.L.2    Gong, Z.3    Lam, T.J.4    Sin, Y.M.5
  • 42
    • 84863630901 scopus 로고    scopus 로고
    • Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics
    • Anderson JL, Marí AR, Braasch I, Amores A, Hohenlohe P, Batzel P, Postlethwait JH. 2012 Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics. PLoS ONE 7, e40701. (doi:10.1371/journal.pone. 0040701)
    • (2012) PLoS ONE , vol.7
    • Anderson, J.L.1    Marí, A.R.2    Braasch, I.3    Amores, A.4    Hohenlohe, P.5    Batzel, P.6    Postlethwait, J.H.7
  • 43
    • 84876798186 scopus 로고    scopus 로고
    • The zebrafish reference genome sequence and its relationship to the human genome
    • Howe K et al. 2013 The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498-503. (doi:10.1038/nature12111)
    • (2013) Nature , vol.496 , pp. 498-503
    • Howe, K.1
  • 44
    • 84908627899 scopus 로고    scopus 로고
    • Wild sex in zebrafish: Loss of the natural sex determinant in domesticated strains
    • Wilson CA et al. 2014 Wild sex in zebrafish: loss of the natural sex determinant in domesticated strains. Genetics 198, 1291-1308. (doi:10.1534/genetics. 114.169284)
    • (2014) Genetics , vol.198 , pp. 1291-1308
    • Wilson, C.A.1
  • 45
    • 84930083595 scopus 로고    scopus 로고
    • The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation
    • Wang Y et al. 2015 The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation. Nat. Genet. 47, 625-631. (doi:10.1038/ng.3280)
    • (2015) Nat. Genet , vol.47 , pp. 625-631
    • Wang, Y.1
  • 46
    • 84943820623 scopus 로고    scopus 로고
    • Creating reference gene annotation for the mouse C57BL6/J genome assembly
    • Mudge JM, Harrow J. 2015 Creating reference gene annotation for the mouse C57BL6/J genome assembly. Mamm. Genome 26, 366-378. (doi:10. 1007/s00335-015-9583-x)
    • (2015) Mamm. Genome , vol.26 , pp. 366-378
    • Mudge, J.M.1    Harrow, J.2
  • 47
    • 16644386470 scopus 로고    scopus 로고
    • The zebrafish genome project: Sequence analysis and annotation. in the zebrafish: Genetics, genomics and informatics
    • (eds HW Detrich, M Westerfield, LI Zon), San Diego, CA: Elsevier Academic Press
    • Jekosch K. 2004 The zebrafish genome project: sequence analysis and annotation. In The zebrafish: genetics, genomics and informatics. Methods in Cell Biology, vol. 77 (eds HW Detrich, M Westerfield, LI Zon), pp. 225-239. San Diego, CA: Elsevier Academic Press.
    • (2004) Methods in Cell Biology , vol.77 , pp. 225-239
    • Jekosch, K.1
  • 48
    • 80054078476 scopus 로고    scopus 로고
    • Fast, scalable generation of high-quality protein multiple sequence alignments using CLUSTAL OMEGA
    • Sievers F et al. 2011 Fast, scalable generation of high-quality protein multiple sequence alignments using CLUSTAL OMEGA. Mol. Syst. Biol. 7, 1-6. (doi:10. 1038/msb.2011.75)
    • (2011) Mol. Syst. Biol , vol.7 , pp. 1-6
    • Sievers, F.1
  • 49
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar RC. 2004 MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113. (doi:10. 1186/1471-2105-5-113)
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 51
    • 67650757433 scopus 로고    scopus 로고
    • TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009 trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973. (doi:10.1093/ bioinformatics/btp348)
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutiérrez, S.1    Silla-Martínez, J.M.2    Gabaldón, T.3
  • 52
    • 79954529507 scopus 로고    scopus 로고
    • ProtTest 3: Fast selection of best-fit models of protein evolution
    • Darriba D, Taboada GL, Doallo R, Posada D. 2011 ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164-1165. (doi:10.1093/bioinformatics/btr088)
    • (2011) Bioinformatics , vol.27 , pp. 1164-1165
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 53
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. 2006 RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690. (doi:10.1093/bioinformatics/ btl446)
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 55
    • 84911391765 scopus 로고    scopus 로고
    • Figmop: A profile HMM to identify genes and bypass troublesome gene models in draft genomes
    • Curran DM, Gilleard JS, Wasmuth JD. 2014 Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes. Bioinformatics 30, 3266-3267. (doi:10.1093/ bioinformatics/btu544)
    • (2014) Bioinformatics , vol.30 , pp. 3266-3267
    • Curran, D.M.1    Gilleard, J.S.2    Wasmuth, J.D.3
  • 57
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • Stanke M, Waack S. 2003 Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19, ii215-ii225. (doi:10.1093/ bioinformatics/btg1080)
    • (2003) Bioinformatics , vol.19 , pp. ii215-ii225
    • Stanke, M.1    Waack, S.2
  • 58
    • 77951682635 scopus 로고    scopus 로고
    • KaKs-calculator 2.0: A toolkit incorporating gammaseries methods and sliding window strategies
    • Wang D, Zhang Y, Zhang Z, Zhu J, Yu J. 2010 KaKs-calculator 2.0: a toolkit incorporating gammaseries methods and sliding window strategies. Genomics Proteomics Bioinformatics 8, 77-80. (doi:10.1016/S1672-0229(10)60008-3)
    • (2010) Genomics Proteomics Bioinformatics , vol.8 , pp. 77-80
    • Wang, D.1    Zhang, Y.2    Zhang, Z.3    Zhu, J.4    Yu, J.5
  • 59
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European molecular biology open software suite
    • Rice P, Longden I, Bleasby A. 2000 EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276-277. (doi:10.1016/S0168- 9525(00)02024-2)
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 60
    • 84862806767 scopus 로고    scopus 로고
    • ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments
    • Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, Dai L. 2012 ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem. Biophys. Res. Commun. 419, 779-781. (doi:10. 1016/j.bbrc.2012.02.101)
    • (2012) Biochem. Biophys. Res. Commun , vol.419 , pp. 779-781
    • Zhang, Z.1    Xiao, J.2    Wu, J.3    Zhang, H.4    Liu, G.5    Wang, X.6    Dai, L.7
  • 61
    • 84885406698 scopus 로고    scopus 로고
    • The USENIX Magazine. See
    • Tange O. 2011 Gnu parallel: the command-line power tool. The USENIX Magazine. See https:// www.usenix.org/publications/login/february-2011- volume-36-number-1/gnu-parallel-command-linepower- tool.
    • (2011) Gnu Parallel: The Command-line Power Tool
    • Tange, O.1
  • 62
    • 34247481878 scopus 로고    scopus 로고
    • IPython: A system for interactive scientific computing
    • Pérez F, Granger BE. 2007 IPython: a system for interactive scientific computing. Comput. Sci. Eng. 9, 21-29. (doi:10.1109/MCSE.2007.53)
    • (2007) Comput. Sci. Eng , vol.9 , pp. 21-29
    • Pérez, F.1    Granger, B.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.