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Volumn 13, Issue 1, 2012, Pages

Controversies in modern evolutionary biology: The imperative for error detection and quality control

Author keywords

Asymmetric evolution; Error detection; Gene duplication; Gene prediction; Quality control

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ARTIFACT; ASYMMETRIC EVOLUTION; DNA SEQUENCE; ERROR; ERROR DETECTION; EVOLUTIONARY RATE; GENE DUPLICATION; HUMAN GENOME; MOLECULAR EVOLUTION; PREDICTION; PROTEIN SEQUENCE ERROR; QUALITY CONTROL; SEQUENCE ANALYSIS; ANIMAL; BIOLOGY; GENOMICS; HUMAN; MOLECULAR GENETICS; PHYLOGENY; REPRODUCIBILITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STANDARD;

EID: 84855268902     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-5     Document Type: Article
Times cited : (30)

References (66)
  • 1
    • 79951475133 scopus 로고    scopus 로고
    • A decade's perspective on DNA sequencing technology
    • 10.1038/nature09796, 21307932
    • Mardis ER. A decade's perspective on DNA sequencing technology. Nature 2011, 470(7333):198-203. 10.1038/nature09796, 21307932.
    • (2011) Nature , vol.470 , Issue.7333 , pp. 198-203
    • Mardis, E.R.1
  • 2
    • 79953716259 scopus 로고    scopus 로고
    • Resolving difficult phylogenetic questions: why more sequences are not enough
    • 10.1371/journal.pbio.1000602, 3057953, 21423652
    • Philippe H, Brinkmann H, Lavrov DV, Littlewood DT, Manuel M, Worheide G, Baurain D. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol 2011, 9(3):e1000602. 10.1371/journal.pbio.1000602, 3057953, 21423652.
    • (2011) PLoS Biol , vol.9 , Issue.3
    • Philippe, H.1    Brinkmann, H.2    Lavrov, D.V.3    Littlewood, D.T.4    Manuel, M.5    Worheide, G.6    Baurain, D.7
  • 3
    • 54149095437 scopus 로고    scopus 로고
    • Estimation of phylogenetic inconsistencies in the three domains of life
    • 10.1093/molbev/msn176, 18701430
    • Soria-Carrasco V, Castresana J. Estimation of phylogenetic inconsistencies in the three domains of life. Mol Biol Evol 2008, 25(11):2319-2329. 10.1093/molbev/msn176, 18701430.
    • (2008) Mol Biol Evol , vol.25 , Issue.11 , pp. 2319-2329
    • Soria-Carrasco, V.1    Castresana, J.2
  • 4
    • 80052858002 scopus 로고    scopus 로고
    • Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer
    • 10.1186/1471-2148-11-259, 3190393, 21923904
    • Stiller JW. Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer. BMC Evol Biol 2011, 11(1):259. 10.1186/1471-2148-11-259, 3190393, 21923904.
    • (2011) BMC Evol Biol , vol.11 , Issue.1 , pp. 259
    • Stiller, J.W.1
  • 5
    • 77955039174 scopus 로고    scopus 로고
    • The origin and early evolution of eukaryotes in the light of phylogenomics
    • Koonin EV. The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biol 2011, 11(5):209.
    • (2011) Genome Biol , vol.11 , Issue.5 , pp. 209
    • Koonin, E.V.1
  • 6
    • 71449100076 scopus 로고    scopus 로고
    • Mapping the tree of life: progress and prospects
    • 10.1128/MMBR.00033-09, 2786576, 19946133
    • Pace NR. Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 2009, 73(4):565-576. 10.1128/MMBR.00033-09, 2786576, 19946133.
    • (2009) Microbiol Mol Biol Rev , vol.73 , Issue.4 , pp. 565-576
    • Pace, N.R.1
  • 7
    • 80052019696 scopus 로고    scopus 로고
    • Estimating the timing of early eukaryotic diversification with multigene molecular clocks
    • 10.1073/pnas.1110633108, 3158185, 21810989
    • Parfrey LW, Lahr DJ, Knoll AH, Katz LA. Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proc Natl Acad Sci USA 2011, 108(33):13624-13629. 10.1073/pnas.1110633108, 3158185, 21810989.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.33 , pp. 13624-13629
    • Parfrey, L.W.1    Lahr, D.J.2    Knoll, A.H.3    Katz, L.A.4
  • 8
    • 78751580323 scopus 로고    scopus 로고
    • On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes
    • 10.1016/j.resmic.2010.10.004, 21034815
    • Desmond E, Brochier-Armanet C, Forterre P, Gribaldo S. On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes. Res Microbiol 2011, 162(1):53-70. 10.1016/j.resmic.2010.10.004, 21034815.
    • (2011) Res Microbiol , vol.162 , Issue.1 , pp. 53-70
    • Desmond, E.1    Brochier-Armanet, C.2    Forterre, P.3    Gribaldo, S.4
  • 9
    • 78649341954 scopus 로고    scopus 로고
    • Different phylogenomic approaches to resolve the evolutionary relationships among model fish species
    • 10.1093/molbev/msq165, 20591844
    • Negrisolo E, Kuhl H, Forcato C, Vitulo N, Reinhardt R, Patarnello T, Bargelloni L. Different phylogenomic approaches to resolve the evolutionary relationships among model fish species. Mol Biol Evol 2010, 27(12):2757-2774. 10.1093/molbev/msq165, 20591844.
    • (2010) Mol Biol Evol , vol.27 , Issue.12 , pp. 2757-2774
    • Negrisolo, E.1    Kuhl, H.2    Forcato, C.3    Vitulo, N.4    Reinhardt, R.5    Patarnello, T.6    Bargelloni, L.7
  • 10
    • 77952482109 scopus 로고    scopus 로고
    • An application of supertree methods to Mammalian mitogenomic sequences
    • 2880846, 20535231
    • Campbell V, Lapointe FJ. An application of supertree methods to Mammalian mitogenomic sequences. Evol Bioinform Online 2010, 6:57-71. 2880846, 20535231.
    • (2010) Evol Bioinform Online , vol.6 , pp. 57-71
    • Campbell, V.1    Lapointe, F.J.2
  • 11
    • 76449092818 scopus 로고    scopus 로고
    • Dogs, cats, and kin: a molecular species-level phylogeny of Carnivora
    • 10.1016/j.ympev.2009.10.033, 19900567
    • Agnarsson I, Kuntner M, May-Collado LJ. Dogs, cats, and kin: a molecular species-level phylogeny of Carnivora. Mol Phylogenet Evol 2010, 54(3):726-745. 10.1016/j.ympev.2009.10.033, 19900567.
    • (2010) Mol Phylogenet Evol , vol.54 , Issue.3 , pp. 726-745
    • Agnarsson, I.1    Kuntner, M.2    May-Collado, L.J.3
  • 12
    • 65449142156 scopus 로고    scopus 로고
    • How confident can we be that orthologs are similar, but paralogs differ?
    • 10.1016/j.tig.2009.03.004, 19368988
    • Studer R, Robinson-Rechavi M. How confident can we be that orthologs are similar, but paralogs differ?. Trends Genet 2009, 25:210-216. 10.1016/j.tig.2009.03.004, 19368988.
    • (2009) Trends Genet , vol.25 , pp. 210-216
    • Studer, R.1    Robinson-Rechavi, M.2
  • 14
    • 77952490857 scopus 로고    scopus 로고
    • Phylogenomics with incomplete taxon coverage: the limits to inference
    • 10.1186/1471-2148-10-155, 2897806, 20500873
    • Sanderson MJ, McMahon MM, Steel M. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evol Biol 2010, 10:155. 10.1186/1471-2148-10-155, 2897806, 20500873.
    • (2010) BMC Evol Biol , vol.10 , pp. 155
    • Sanderson, M.J.1    McMahon, M.M.2    Steel, M.3
  • 15
    • 77950949307 scopus 로고    scopus 로고
    • Dealing with missing values in large-scale studies: microarray data imputation and beyond
    • 10.1093/bib/bbp059, 19965979
    • Aittokallio T. Dealing with missing values in large-scale studies: microarray data imputation and beyond. Brief Bioinform 2010, 11(2):253-264. 10.1093/bib/bbp059, 19965979.
    • (2010) Brief Bioinform , vol.11 , Issue.2 , pp. 253-264
    • Aittokallio, T.1
  • 16
    • 79959406807 scopus 로고    scopus 로고
    • Identification of metabolic network models from incomplete high-throughput datasets
    • Berthoumieux S, Brilli M, de Jong H, Kahn D, Cinquemani E. Identification of metabolic network models from incomplete high-throughput datasets. Bioinformatics 2010, 27(13):i186-195.
    • (2010) Bioinformatics , vol.27 , Issue.13
    • Berthoumieux, S.1    Brilli, M.2    de Jong, H.3    Kahn, D.4    Cinquemani, E.5
  • 17
    • 39649084637 scopus 로고    scopus 로고
    • Bioinformatics challenges of new sequencing technology
    • 10.1016/j.tig.2007.12.006, 2680276, 18262676
    • Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends Genet 2008, 24:142-149. 10.1016/j.tig.2007.12.006, 2680276, 18262676.
    • (2008) Trends Genet , vol.24 , pp. 142-149
    • Pop, M.1    Salzberg, S.L.2
  • 18
    • 79953051389 scopus 로고    scopus 로고
    • Genome builders face the competition
    • 10.1038/471425a, 21430748
    • Hayden EC. Genome builders face the competition. Nature 2011, 471(7339):425. 10.1038/471425a, 21430748.
    • (2011) Nature , vol.471 , Issue.7339 , pp. 425
    • Hayden, E.C.1
  • 19
    • 79952065370 scopus 로고    scopus 로고
    • Error and error mitigation in low-coverage genome assemblies
    • 10.1371/journal.pone.0017034, 3038916, 21340033
    • Hubisz M, Lin M, Kellis M, Siepel A. Error and error mitigation in low-coverage genome assemblies. PLOS One 2011, 6:e17034. 10.1371/journal.pone.0017034, 3038916, 21340033.
    • (2011) PLOS One , vol.6
    • Hubisz, M.1    Lin, M.2    Kellis, M.3    Siepel, A.4
  • 20
    • 79951794116 scopus 로고    scopus 로고
    • Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses
    • Vilella AJ, Birney E, Flicek P, Herrero J. Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses. Genome Biol 2011, 12(2):401.
    • (2011) Genome Biol , vol.12 , Issue.2 , pp. 401
    • Vilella, A.J.1    Birney, E.2    Flicek, P.3    Herrero, J.4
  • 21
    • 74049094093 scopus 로고    scopus 로고
    • The effect of sequencing errors on metagenomic gene prediction
    • 10.1186/1471-2164-10-520, 2781827, 19909532
    • Hoff KJ. The effect of sequencing errors on metagenomic gene prediction. BMC Genomics 2009, 10:520. 10.1186/1471-2164-10-520, 2781827, 19909532.
    • (2009) BMC Genomics , vol.10 , pp. 520
    • Hoff, K.J.1
  • 23
    • 77957278356 scopus 로고    scopus 로고
    • Between a chicken and a grape: estimating the number of human genes
    • Pertea M, Salzberg SL. Between a chicken and a grape: estimating the number of human genes. Genome Biol 2011, 11(5):206.
    • (2011) Genome Biol , vol.11 , Issue.5 , pp. 206
    • Pertea, M.1    Salzberg, S.L.2
  • 24
    • 37249005195 scopus 로고    scopus 로고
    • Steady progress and recent breakthroughs in the accuracy of automated genome annotation
    • 10.1038/nrg2220, 18087260
    • Brent MR. Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet 2008, 9(1):62-73. 10.1038/nrg2220, 18087260.
    • (2008) Nat Rev Genet , vol.9 , Issue.1 , pp. 62-73
    • Brent, M.R.1
  • 25
    • 60749118171 scopus 로고    scopus 로고
    • Identifying protein-coding genes in genomic sequences
    • 10.1186/gb-2009-10-1-201, 2687780, 19226436
    • Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigo R. Identifying protein-coding genes in genomic sequences. Genome Biol 2009, 10(1):201. 10.1186/gb-2009-10-1-201, 2687780, 19226436.
    • (2009) Genome Biol , vol.10 , Issue.1 , pp. 201
    • Harrow, J.1    Nagy, A.2    Reymond, A.3    Alioto, T.4    Patthy, L.5    Antonarakis, S.E.6    Guigo, R.7
  • 26
    • 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
  • 27
    • 76149130971 scopus 로고    scopus 로고
    • Alternative splicing: global insights
    • 10.1111/j.1742-4658.2009.07521.x, 20082635
    • Hallegger M, Llorian M, Smith CW. Alternative splicing: global insights. Febs J 2010, 277(4):856-866. 10.1111/j.1742-4658.2009.07521.x, 20082635.
    • (2010) Febs J , vol.277 , Issue.4 , pp. 856-866
    • Hallegger, M.1    Llorian, M.2    Smith, C.W.3
  • 28
    • 72149107901 scopus 로고    scopus 로고
    • Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment
    • 2817407, 20333182
    • Schneider A, Souvorov A, Sabath N, Landan G, Gonnet GH, Graur D. Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol Evol 2009, 1:114-118. 2817407, 20333182.
    • (2009) Genome Biol Evol , vol.1 , pp. 114-118
    • Schneider, A.1    Souvorov, A.2    Sabath, N.3    Landan, G.4    Gonnet, G.H.5    Graur, D.6
  • 30
    • 36549038087 scopus 로고    scopus 로고
    • Consequences of genome duplication
    • 10.1016/j.gde.2007.09.007, 18006297
    • Semon M, Wolfe KH. Consequences of genome duplication. Curr Opin Genet Dev 2007, 17(6):505-512. 10.1016/j.gde.2007.09.007, 18006297.
    • (2007) Curr Opin Genet Dev , vol.17 , Issue.6 , pp. 505-512
    • Semon, M.1    Wolfe, K.H.2
  • 31
    • 68149176813 scopus 로고    scopus 로고
    • Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates
    • 10.1101/gr.086827.108, 2720184, 19439512
    • Kassahn KS, Dang VT, Wilkins SJ, Perkins AC, Ragan MA. Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates. Genome Res 2009, 19(8):1404-1418. 10.1101/gr.086827.108, 2720184, 19439512.
    • (2009) Genome Res , vol.19 , Issue.8 , pp. 1404-1418
    • Kassahn, K.S.1    Dang, V.T.2    Wilkins, S.J.3    Perkins, A.C.4    Ragan, M.A.5
  • 32
    • 79951559649 scopus 로고    scopus 로고
    • The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics
    • 10.1186/1745-6150-6-11, 3052240, 21333002
    • Levasseur A, Pontarotti P. The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics. Biol Direct 2011, 6:11. 10.1186/1745-6150-6-11, 3052240, 21333002.
    • (2011) Biol Direct , vol.6 , pp. 11
    • Levasseur, A.1    Pontarotti, P.2
  • 33
    • 33344470194 scopus 로고    scopus 로고
    • Diagnosing duplications--can it be done?
    • 10.1016/j.tig.2006.01.002, 16442663
    • Durand D, Hoberman R. Diagnosing duplications--can it be done?. Trends Genet 2006, 22(3):156-164. 10.1016/j.tig.2006.01.002, 16442663.
    • (2006) Trends Genet , vol.22 , Issue.3 , pp. 156-164
    • Durand, D.1    Hoberman, R.2
  • 34
    • 56549119570 scopus 로고    scopus 로고
    • Turning a hobby into a job: how duplicated genes find new functions
    • 10.1038/nrg2482, 19015656
    • Conant GC, Wolfe KH. Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 2008, 9(12):938-950. 10.1038/nrg2482, 19015656.
    • (2008) Nat Rev Genet , vol.9 , Issue.12 , pp. 938-950
    • Conant, G.C.1    Wolfe, K.H.2
  • 35
    • 70349445554 scopus 로고    scopus 로고
    • Duplication mechanism and disruptions in flanking regions determine the fate of Mammalian gene duplicates
    • 10.1089/cmb.2009.0074, 19772436
    • Jun J, Ryvkin P, Hemphill E, Nelson C. Duplication mechanism and disruptions in flanking regions determine the fate of Mammalian gene duplicates. J Comput Biol 2009, 16(9):1253-1266. 10.1089/cmb.2009.0074, 19772436.
    • (2009) J Comput Biol , vol.16 , Issue.9 , pp. 1253-1266
    • Jun, J.1    Ryvkin, P.2    Hemphill, E.3    Nelson, C.4
  • 37
    • 79953307693 scopus 로고    scopus 로고
    • A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives
    • 10.1371/journal.pone.0018093, 3069049, 21483869
    • Thompson JD, Linard B, Lecompte O, Poch O. A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One 2011, 6(3):e18093. 10.1371/journal.pone.0018093, 3069049, 21483869.
    • (2011) PLoS One , vol.6 , Issue.3
    • Thompson, J.D.1    Linard, B.2    Lecompte, O.3    Poch, O.4
  • 38
    • 77951813504 scopus 로고    scopus 로고
    • Genome assembly quality: Assessment and improvement using the neutral indel model
    • 10.1101/gr.096966.109, 2860169, 20305016
    • Meader S, Hillier L, Locke D, Ponting C, Lunter G. Genome assembly quality: Assessment and improvement using the neutral indel model. Genome Res 2010, 20:675-684. 10.1101/gr.096966.109, 2860169, 20305016.
    • (2010) Genome Res , vol.20 , pp. 675-684
    • Meader, S.1    Hillier, L.2    Locke, D.3    Ponting, C.4    Lunter, G.5
  • 39
    • 28444453303 scopus 로고    scopus 로고
    • Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data
    • 10.1093/bioinformatics/bti711, 16216829
    • Boyer F, Morgat A, Labarre L, Pothier J, Viari A. Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data. Bioinformatics 2005, 21(23):4209-4215. 10.1093/bioinformatics/bti711, 16216829.
    • (2005) Bioinformatics , vol.21 , Issue.23 , pp. 4209-4215
    • Boyer, F.1    Morgat, A.2    Labarre, L.3    Pothier, J.4    Viari, A.5
  • 40
    • 57149139413 scopus 로고    scopus 로고
    • Syntenator: multiple gene order alignments with a gene-specific scoring function
    • 10.1186/1748-7188-3-14, 2590594, 18990215
    • Rodelsperger C, Dieterich C. Syntenator: multiple gene order alignments with a gene-specific scoring function. Algorithms Mol Biol 2008, 3:14. 10.1186/1748-7188-3-14, 2590594, 18990215.
    • (2008) Algorithms Mol Biol , vol.3 , pp. 14
    • Rodelsperger, C.1    Dieterich, C.2
  • 41
    • 74549156240 scopus 로고    scopus 로고
    • Identification of mammalian orthologs using local synteny
    • 10.1186/1471-2164-10-630, 2807883, 20030836
    • Jun J, Mandoiu I, Nelson C. Identification of mammalian orthologs using local synteny. BMC Genomics 2009, 10:630. 10.1186/1471-2164-10-630, 2807883, 20030836.
    • (2009) BMC Genomics , vol.10 , pp. 630
    • Jun, J.1    Mandoiu, I.2    Nelson, C.3
  • 42
    • 58349111875 scopus 로고    scopus 로고
    • AmiGO: online access to ontology and annotation data
    • 10.1093/bioinformatics/btn615, 2639003, 19033274
    • Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S. AmiGO: online access to ontology and annotation data. Bioinformatics 2009, 25(2):288-289. 10.1093/bioinformatics/btn615, 2639003, 19033274.
    • (2009) Bioinformatics , vol.25 , Issue.2 , pp. 288-289
    • Carbon, S.1    Ireland, A.2    Mungall, C.J.3    Shu, S.4    Marshall, B.5    Lewis, S.6
  • 43
    • 79955771442 scopus 로고    scopus 로고
    • GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns
    • 10.1093/bioinformatics/btr142, 21421553
    • Yang X, Li J, Lee Y, Lussier YA. GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. Bioinformatics 2011, 27(10):1444-1446. 10.1093/bioinformatics/btr142, 21421553.
    • (2011) Bioinformatics , vol.27 , Issue.10 , pp. 1444-1446
    • Yang, X.1    Li, J.2    Lee, Y.3    Lussier, Y.A.4
  • 44
    • 80052824121 scopus 로고    scopus 로고
    • MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons
    • 10.1371/journal.pone.0022594, 3174933, 21949676
    • Ranwez V, Harispe S, Delsuc F, Douzery EJ. MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. Plos One 2011, 6(9):e22594. 10.1371/journal.pone.0022594, 3174933, 21949676.
    • (2011) Plos One , vol.6 , Issue.9
    • Ranwez, V.1    Harispe, S.2    Delsuc, F.3    Douzery, E.J.4
  • 46
    • 77957190385 scopus 로고    scopus 로고
    • Assessment of orthologous splicing isoforms in human and mouse orthologous genes
    • 10.1186/1471-2164-11-534, 3091683, 20920313
    • Zambelli F, Pavesi G, Gissi C, Horner DS, Pesole G. Assessment of orthologous splicing isoforms in human and mouse orthologous genes. BMC Genomics 2010, 11:534. 10.1186/1471-2164-11-534, 3091683, 20920313.
    • (2010) BMC Genomics , vol.11 , pp. 534
    • Zambelli, F.1    Pavesi, G.2    Gissi, C.3    Horner, D.S.4    Pesole, G.5
  • 47
    • 33749342164 scopus 로고    scopus 로고
    • Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human
    • 10.1371/journal.pcbi.0020133, 1584324, 17009864
    • Goodstadt L, Ponting CP. Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol 2006, 2(9):e133. 10.1371/journal.pcbi.0020133, 1584324, 17009864.
    • (2006) PLoS Comput Biol , vol.2 , Issue.9
    • Goodstadt, L.1    Ponting, C.P.2
  • 48
    • 45549101445 scopus 로고    scopus 로고
    • Designating eukaryotic orthology via processed transcription units
    • 10.1093/nar/gkn227, 2425467, 18445630
    • Ho MR, Jang WJ, Chen CH, Ch'ang LY, Lin WC. Designating eukaryotic orthology via processed transcription units. Nucleic Acids Res 2008, 36(10):3436-3442. 10.1093/nar/gkn227, 2425467, 18445630.
    • (2008) Nucleic Acids Res , vol.36 , Issue.10 , pp. 3436-3442
    • Ho, M.R.1    Jang, W.J.2    Chen, C.H.3    Ch'ang, L.Y.4    Lin, W.C.5
  • 49
    • 34250659350 scopus 로고    scopus 로고
    • More genes underwent positive selection in chimpanzee evolution than in human evolution
    • 10.1073/pnas.0701705104, 1863478, 17449636
    • Bakewell MA, Shi P, Zhang J. More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci USA 2007, 104(18):7489-7494. 10.1073/pnas.0701705104, 1863478, 17449636.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.18 , pp. 7489-7494
    • Bakewell, M.A.1    Shi, P.2    Zhang, J.3
  • 50
    • 66049087893 scopus 로고    scopus 로고
    • The difficulty of avoiding false positives in genome scans for natural selection
    • 10.1101/gr.086512.108, 2675981, 19411606
    • Mallick S, Gnerre S, Muller P, Reich D. The difficulty of avoiding false positives in genome scans for natural selection. Genome Res 2009, 19(5):922-933. 10.1101/gr.086512.108, 2675981, 19411606.
    • (2009) Genome Res , vol.19 , Issue.5 , pp. 922-933
    • Mallick, S.1    Gnerre, S.2    Muller, P.3    Reich, D.4
  • 52
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • 10.1006/jmbi.2000.5197, 11743721
    • Remm M, Storm CE, Sonnhammer EL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 2001, 314(5):1041-1052. 10.1006/jmbi.2000.5197, 11743721.
    • (2001) J Mol Biol , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 53
    • 66049138497 scopus 로고    scopus 로고
    • Adaptive evolution of young gene duplicates in mammals
    • 10.1101/gr.085951.108, 2675974, 19411603
    • Han MV, Demuth JP, McGrath CL, Casola C, Hahn MW. Adaptive evolution of young gene duplicates in mammals. Genome Res 2009, 19(5):859-867. 10.1101/gr.085951.108, 2675974, 19411603.
    • (2009) Genome Res , vol.19 , Issue.5 , pp. 859-867
    • Han, M.V.1    Demuth, J.P.2    McGrath, C.L.3    Casola, C.4    Hahn, M.W.5
  • 54
    • 62549166268 scopus 로고    scopus 로고
    • Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease
    • 10.1159/000184688, 2920180, 19287135
    • de Smith AJ, Walters RG, Froguel P, Blakemore AI. Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease. Cytogenet Genome Res 2008, 123(1-4):17-26. 10.1159/000184688, 2920180, 19287135.
    • (2008) Cytogenet Genome Res , vol.123 , Issue.1-4 , pp. 17-26
    • de Smith, A.J.1    Walters, R.G.2    Froguel, P.3    Blakemore, A.I.4
  • 56
    • 78651319979 scopus 로고    scopus 로고
    • Ongoing and future developments at the Universal Protein Resource
    • UniProt, Database
    • UniProt Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 2011, (39 Database):D214-219. UniProt.
    • (2011) Nucleic Acids Res , Issue.39
  • 57
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 58
    • 0033675717 scopus 로고    scopus 로고
    • Ballast: blast post-processing based on locally conserved segments
    • 10.1093/bioinformatics/16.9.750, 11108697
    • Plewniak F, Thompson JD, Poch O. Ballast: blast post-processing based on locally conserved segments. Bioinformatics 2000, 16:750-759. 10.1093/bioinformatics/16.9.750, 11108697.
    • (2000) Bioinformatics , vol.16 , pp. 750-759
    • Plewniak, F.1    Thompson, J.D.2    Poch, O.3
  • 59
    • 0034255358 scopus 로고    scopus 로고
    • DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches
    • 10.1093/nar/28.15.2919, 102675, 10908355
    • Thompson J, Plewniak F, Thierry J, O P. DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res 2000, 28:2919-2926. 10.1093/nar/28.15.2919, 102675, 10908355.
    • (2000) Nucleic Acids Res , vol.28 , pp. 2919-2926
    • Thompson, J.1    Plewniak, F.2    Thierry, J.3    O, P.4
  • 60
    • 0038391401 scopus 로고    scopus 로고
    • RASCAL: rapid scanning and correction of multiple sequence alignments
    • 10.1093/bioinformatics/btg133, 12801878
    • Thompson JD, Thierry JC, Poch O. RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics 2003, 19:1155-1161. 10.1093/bioinformatics/btg133, 12801878.
    • (2003) Bioinformatics , vol.19 , pp. 1155-1161
    • Thompson, J.D.1    Thierry, J.C.2    Poch, O.3
  • 61
    • 2542558960 scopus 로고    scopus 로고
    • LEON: multiple aLignment Evaluation Of Neighbours
    • 10.1093/nar/gkh294, 390283, 14982955
    • Thompson JD, Prigent V, Poch O. LEON: multiple aLignment Evaluation Of Neighbours. Nucleic Acids Res 2004, 32:1298-1307. 10.1093/nar/gkh294, 390283, 14982955.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1298-1307
    • Thompson, J.D.1    Prigent, V.2    Poch, O.3
  • 62
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • 10.1093/bib/bbn013, 18372315
    • Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008, 9:286-298. 10.1093/bib/bbn013, 18372315.
    • (2008) Brief Bioinform , vol.9 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 63
    • 33847138105 scopus 로고    scopus 로고
    • MACSIMS: multiple alignment of complete sequences information management system
    • 10.1186/1471-2105-7-318, 1539025, 16792820
    • Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, Plewniak F, Poch O. MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics 2006, 7:318. 10.1186/1471-2105-7-318, 1539025, 16792820.
    • (2006) BMC Bioinformatics , vol.7 , pp. 318
    • Thompson, J.D.1    Muller, A.2    Waterhouse, A.3    Procter, J.4    Barton, G.J.5    Plewniak, F.6    Poch, O.7
  • 65
    • 0029897488 scopus 로고    scopus 로고
    • PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames
    • 10.1093/nar/24.14.2730, 145991, 8759004
    • Birney E, Thompson J, Gibson T. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Res 1996, 24(14):2730-2739. 10.1093/nar/24.14.2730, 145991, 8759004.
    • (1996) Nucleic Acids Res , vol.24 , Issue.14 , pp. 2730-2739
    • Birney, E.1    Thompson, J.2    Gibson, T.3
  • 66
    • 33846642694 scopus 로고    scopus 로고
    • Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
    • 10.1186/1471-2105-7-529, 1762028, 17147817
    • Dessimoz C, Gil M, Schneider A, Gonnet G. Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences. BMC Bioinformatics 2006, 7:529. 10.1186/1471-2105-7-529, 1762028, 17147817.
    • (2006) BMC Bioinformatics , vol.7 , pp. 529
    • Dessimoz, C.1    Gil, M.2    Schneider, A.3    Gonnet, G.4


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