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Volumn 10, Issue , 2009, Pages

Revisiting the missing protein-coding gene catalog of the domestic dog

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DOG; DOMESTIC ANIMAL; GENE FUNCTION; GENE IDENTIFICATION; GENE LOSS; GENE MAPPING; GENE STRUCTURE; GENETIC CODE; GENETIC CONSERVATION; NONHUMAN; ORTHOLOGY; PSEUDOGENE; SPECIES DIFFERENCE; SYNTENY; ANIMAL; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; GENOME; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EID: 60849083233     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-62     Document Type: Article
Times cited : (18)

References (60)
  • 5
    • 37249005195 scopus 로고    scopus 로고
    • Steady progress and recent breakthroughs in the accuracy of automated genome annotation
    • 18087260
    • Brent MR Steady progress and recent breakthroughs in the accuracy of automated genome annotation Nat Rev Genet 2008, 9(1):62-73. 18087260
    • (2008) Nat Rev Genet , vol.9 , Issue.1 , pp. 62-73
    • Brent, M.R.1
  • 6
    • 2442713832 scopus 로고    scopus 로고
    • GeneWise and Genomewise
    • 479130 15123596
    • Birney E Clamp M Durbin R GeneWise and Genomewise Genome Res 2004, 14(5):988-995. 479130 15123596
    • (2004) Genome Res , vol.14 , Issue.5 , pp. 988-995
    • Birney, E.1    Clamp, M.2    Durbin, R.3
  • 7
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • 11473003
    • Korf I Flicek P Duan D Brent MR Integrating genomic homology into gene structure prediction Bioinformatics 2001, 17(Suppl 1):140-148. 11473003
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 9
    • 20744436518 scopus 로고    scopus 로고
    • Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases
    • 15713731
    • Dufayard JF Duret L Penel S Gouy M Rechenmann F Perriere G Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases Bioinformatics 2005, 21(11):2596-2603. 15713731
    • (2005) Bioinformatics , vol.21 , Issue.11 , pp. 2596-2603
    • Dufayard, J.F.1    Duret, L.2    Penel, S.3    Gouy, M.4    Rechenmann, F.5    Perriere, G.6
  • 10
    • 33749342164 scopus 로고    scopus 로고
    • Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human
    • 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. 1584324 17009864
    • (2006) PLoS Comput Biol , vol.2 , Issue.9
    • Goodstadt, L.1    Ponting, C.P.2
  • 11
    • 33645798112 scopus 로고    scopus 로고
    • Genome-wide identification of human functional DNA using a neutral indel model
    • 1326222 16410828
    • Lunter G Ponting CP Hein J Genome-wide identification of human functional DNA using a neutral indel model PLoS Comput Biol 2006, 2(1):e5. 1326222 16410828
    • (2006) PLoS Comput Biol , vol.2 , Issue.1
    • Lunter, G.1    Ponting, C.P.2    Hein, J.3
  • 13
    • 33847255798 scopus 로고    scopus 로고
    • AutoGRAPH: An interactive web server for automating and visualizing comparative genome maps
    • 17145741
    • Derrien T Andre C Galibert F Hitte C AutoGRAPH: An interactive web server for automating and visualizing comparative genome maps Bioinformatics 2007, 23(4):498-499. 17145741
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 498-499
    • Derrien, T.1    Andre, C.2    Galibert, F.3    Hitte, C.4
  • 14
    • 33645766047 scopus 로고    scopus 로고
    • The fragile breakage versus random breakage models of chromosome evolution
    • 1378107 16501665
    • Peng Q Pevzner PA Tesler G The fragile breakage versus random breakage models of chromosome evolution PLoS Comput Biol 2006, 2(2):e14. 1378107 16501665
    • (2006) PLoS Comput Biol , vol.2 , Issue.2
    • Peng, Q.1    Pevzner, P.A.2    Tesler, G.3
  • 15
    • 0036211065 scopus 로고    scopus 로고
    • GRIMM: Genome rearrangements web server
    • Tesler G GRIMM: Genome rearrangements web server Bioinformatics 2002 18 3 492 493 11934753
    • (2002) Bioinformatics , vol.18 , pp. 492-493
    • Tesler, G.1
  • 20
    • 38549148421 scopus 로고    scopus 로고
    • Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
    • 2099592 17989258
    • Heger A Ponting CP Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes Genome Res 2007, 17(12):1837-1849. 2099592 17989258
    • (2007) Genome Res , vol.17 , Issue.12 , pp. 1837-1849
    • Heger, A.1    Ponting, C.P.2
  • 23
    • 0036889686 scopus 로고    scopus 로고
    • Orthology, paralogy and proposed classification for paralog subtypes
    • 12446146
    • Sonnhammer EL Koonin EV Orthology, paralogy and proposed classification for paralog subtypes Trends Genet 2002, 18(12):619-620. 12446146
    • (2002) Trends Genet , vol.18 , Issue.12 , pp. 619-620
    • Sonnhammer, E.L.1    Koonin, E.V.2
  • 26
    • 1842427830 scopus 로고    scopus 로고
    • The evolutionary dynamics of eukaryotic gene order
    • 15131653
    • Hurst LD Pal C Lercher MJ The evolutionary dynamics of eukaryotic gene order Nat Rev Genet 2004, 5(4):299-310. 15131653
    • (2004) Nat Rev Genet , vol.5 , Issue.4 , pp. 299-310
    • Hurst, L.D.1    Pal, C.2    Lercher, M.J.3
  • 27
    • 37249085295 scopus 로고    scopus 로고
    • Genome-scale analysis of positionally relocated genes
    • 2099595 17989252
    • Bhutkar A Russo SM Smith TF Gelbart WM Genome-scale analysis of positionally relocated genes Genome Res 2007, 17(12):1880-1887. 2099595 17989252
    • (2007) Genome Res , vol.17 , Issue.12 , pp. 1880-1887
    • Bhutkar, A.1    Russo, S.M.2    Smith, T.F.3    Gelbart, W.M.4
  • 28
    • 40049091292 scopus 로고    scopus 로고
    • Using native and syntenically mapped cDNA alignments to improve de novo gene finding
    • 18218656
    • Stanke M Diekhans M Baertsch R Haussler D Using native and syntenically mapped cDNA alignments to improve de novo gene finding Bioinformatics 2008, 24(5):637-644. 18218656
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 637-644
    • Stanke, M.1    Diekhans, M.2    Baertsch, R.3    Haussler, D.4
  • 29
    • 33745173827 scopus 로고    scopus 로고
    • Iterative gene prediction and pseudogene removal improves genome annotation
    • 1457044 16651666
    • van Baren MJ Brent MR Iterative gene prediction and pseudogene removal improves genome annotation Genome Res 2006, 16(5):678-685. 1457044 16651666
    • (2006) Genome Res , vol.16 , Issue.5 , pp. 678-685
    • van Baren, M.J.1    Brent, M.R.2
  • 31
    • 2942550697 scopus 로고    scopus 로고
    • GOTree Machine (GOTM): A web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies
    • 373441 14975175
    • Zhang B Schmoyer D Kirov S Snoddy J GOTree Machine (GOTM): A web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies BMC Bioinformatics 2004, 5:16. 373441 14975175
    • (2004) BMC Bioinformatics , vol.5 , pp. 16
    • Zhang, B.1    Schmoyer, D.2    Kirov, S.3    Snoddy, J.4
  • 32
    • 34248596154 scopus 로고    scopus 로고
    • An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes
    • 1899124 17495010
    • Goodstadt L Heger A Webber C Ponting CP An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes Genome Res 2007, 17(7):969-981. 1899124 17495010
    • (2007) Genome Res , vol.17 , Issue.7 , pp. 969-981
    • Goodstadt, L.1    Heger, A.2    Webber, C.3    Ponting, C.P.4
  • 33
    • 0037264074 scopus 로고    scopus 로고
    • Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
    • 430962 12529304
    • Pevzner P Tesler G Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes Genome Res 2003, 13(1):37-45. 430962 12529304
    • (2003) Genome Res , vol.13 , Issue.1 , pp. 37-45
    • Pevzner, P.1    Tesler, G.2
  • 34
    • 36949006683 scopus 로고    scopus 로고
    • Are there rearrangement hotspots in the human genome?
    • 2065889 17997591
    • Alekseyev MA Pevzner PA Are there rearrangement hotspots in the human genome? PLoS Comput Biol 2007, 3(11):e209. 2065889 17997591
    • (2007) PLoS Comput Biol , vol.3 , Issue.11
    • Alekseyev, M.A.1    Pevzner, P.A.2
  • 35
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • 553969 15713233
    • Slater GS Birney E Automated generation of heuristics for biological sequence comparison BMC Bioinformatics 2005, 6:31. 553969 15713233
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.1    Birney, E.2
  • 36
    • 1342263801 scopus 로고    scopus 로고
    • Gene structure conservation aids similarity based gene prediction
    • 373336 14764925
    • Meyer IM Durbin R Gene structure conservation aids similarity based gene prediction Nucleic Acids Res 2004, 32(2):776-783. 373336 14764925
    • (2004) Nucleic Acids Res , vol.32 , Issue.2 , pp. 776-783
    • Meyer, I.M.1    Durbin, R.2
  • 38
    • 36549003965 scopus 로고    scopus 로고
    • InterPro and InterProScan: Tools for protein sequence classification and comparison
    • 18025686
    • Mulder N Apweiler R InterPro and InterProScan: Tools for protein sequence classification and comparison Methods Mol Biol 2007, 396:59-70. 18025686
    • (2007) Methods Mol Biol , vol.396 , pp. 59-70
    • Mulder, N.1    Apweiler, R.2
  • 39
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • 16301204
    • Arnold K Bordoli L Kopp J Schwede T The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling Bioinformatics 2006, 22(2):195-201. 16301204
    • (2006) Bioinformatics , vol.22 , Issue.2 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 40
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • 1538787
    • Luthy R Bowie JU Eisenberg D Assessment of protein models with three-dimensional profiles Nature 1992, 356(6364):83-85. 1538787
    • (1992) Nature , vol.356 , Issue.6364 , pp. 83-85
    • Luthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 41
    • 33644549987 scopus 로고    scopus 로고
    • Nested genes in the human genome
    • 16084061
    • Yu P Ma D Xu M Nested genes in the human genome Genomics 2005, 86(4):414-422. 16084061
    • (2005) Genomics , vol.86 , Issue.4 , pp. 414-422
    • Yu, P.1    Ma, D.2    Xu, M.3
  • 42
    • 0348013073 scopus 로고    scopus 로고
    • A genome-wide survey of human pseudogenes
    • 403797 14656963
    • Torrents D Suyama M Zdobnov E Bork P A genome-wide survey of human pseudogenes Genome Res 2003, 13(12):2559-2567. 403797 14656963
    • (2003) Genome Res , vol.13 , Issue.12 , pp. 2559-2567
    • Torrents, D.1    Suyama, M.2    Zdobnov, E.3    Bork, P.4
  • 43
    • 33749997527 scopus 로고    scopus 로고
    • Systematic identification of pseudogenes through whole genome expression evidence profiling
    • 1636364 16945953
    • Yao A Charlab R Li P Systematic identification of pseudogenes through whole genome expression evidence profiling Nucleic Acids Res 2006, 34(16):4477-4485. 1636364 16945953
    • (2006) Nucleic Acids Res , vol.34 , Issue.16 , pp. 4477-4485
    • Yao, A.1    Charlab, R.2    Li, P.3
  • 45
    • 47349109604 scopus 로고    scopus 로고
    • Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations
    • 2435553 18505555
    • Hallstrom BM Janke A Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations BMC Evol Biol 2008, 8:162. 2435553 18505555
    • (2008) BMC Evol Biol , vol.8 , pp. 162
    • Hallstrom, B.M.1    Janke, A.2
  • 46
    • 0031110886 scopus 로고    scopus 로고
    • From gene to organismal phylogeny: Reconciled trees and the gene tree/ species tree problem
    • 9126565
    • Page RD Charleston MA From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem Mol Phylogenet Evol 1997, 7(2):231-240. 9126565
    • (1997) Mol Phylogenet Evol , vol.7 , Issue.2 , pp. 231-240
    • Page, R.D.1    Charleston, M.A.2
  • 47
    • 0142124263 scopus 로고    scopus 로고
    • Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    • 403683 14525925
    • Krylov DM Wolf YI Rogozin IB Koonin EV Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution Genome Res 2003, 13(10):2229-2235. 403683 14525925
    • (2003) Genome Res , vol.13 , Issue.10 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 48
    • 23144464901 scopus 로고    scopus 로고
    • WebGestalt: An integrated system for exploring gene sets in various biological contexts
    • 1160236 15980575
    • Zhang B Kirov S Snoddy J WebGestalt: An integrated system for exploring gene sets in various biological contexts Nucleic Acids Res 2005, 33: Web Server W741-748. 1160236 15980575
    • (2005) Nucleic Acids Res
    • Zhang, B.1    Kirov, S.2    Snoddy, J.3
  • 49
    • 0035115845 scopus 로고    scopus 로고
    • T-targets: Clues to understanding the functions of T-box proteins
    • 11148447
    • Tada M Smith JC T-targets: Clues to understanding the functions of T-box proteins Dev Growth Differ 2001, 43(1):1-11. 11148447
    • (2001) Dev Growth Differ , vol.43 , Issue.1 , pp. 1-11
    • Tada, M.1    Smith, J.C.2
  • 52
    • 33745051802 scopus 로고    scopus 로고
    • Reference based annotation with GeneMapper
    • 1557983 16600017
    • Chatterji S Pachter L Reference based annotation with GeneMapper Genome Biol 2006, 7(4):R29. 1557983 16600017
    • (2006) Genome Biol , vol.7 , Issue.4
    • Chatterji, S.1    Pachter, L.2
  • 54
    • 37849032744 scopus 로고    scopus 로고
    • Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage
    • 2134963 18085818
    • Zhu J Sanborn JZ Diekhans M Lowe CB Pringle TH Haussler D Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage PLoS Comput Biol 2007, 3(12):e247. 2134963 18085818
    • (2007) PLoS Comput Biol , vol.3 , Issue.12
    • Zhu, J.1    Sanborn, J.Z.2    Diekhans, M.3    Lowe, C.B.4    Pringle, T.H.5    Haussler, D.6
  • 55
    • 34248153305 scopus 로고    scopus 로고
    • Selection for tameness modulates the expression of heme related genes in silver foxes
    • 1858698 17439650
    • Lindberg J Bjornerfeldt S Bakken M Vila C Jazin E Saetre P Selection for tameness modulates the expression of heme related genes in silver foxes Behav Brain Funct 2007, 3:18. 1858698 17439650
    • (2007) Behav Brain Funct , vol.3 , pp. 18
    • Lindberg, J.1    Bjornerfeldt, S.2    Bakken, M.3    Vila, C.4    Jazin, E.5    Saetre, P.6
  • 56
    • 33947617347 scopus 로고    scopus 로고
    • Backup without redundancy: Genetic interactions reveal the cost of duplicate gene loss
    • 1847942 17389874
    • Ihmels J Collins SR Schuldiner M Krogan NJ Weissman JS Backup without redundancy: Genetic interactions reveal the cost of duplicate gene loss Mol Syst Biol 2007, 3:86. 1847942 17389874
    • (2007) Mol Syst Biol , vol.3 , pp. 86
    • Ihmels, J.1    Collins, S.R.2    Schuldiner, M.3    Krogan, N.J.4    Weissman, J.S.5
  • 57
    • 36148960409 scopus 로고    scopus 로고
    • The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation
    • 17957399
    • Hughes T Liberles DA The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation J Mol Evol 2007, 65(5):574-588. 17957399
    • (2007) J Mol Evol , vol.65 , Issue.5 , pp. 574-588
    • Hughes, T.1    Liberles, D.A.2
  • 59
    • 0029259085 scopus 로고
    • Maximum discrimination hidden Markov models of sequence consensus
    • 7497123
    • Eddy SR Mitchison G Durbin R Maximum discrimination hidden Markov models of sequence consensus J Comput Biol 1995, 2(1):9-23. 7497123
    • (1995) J Comput Biol , vol.2 , Issue.1 , pp. 9-23
    • Eddy, S.R.1    Mitchison, G.2    Durbin, R.3
  • 60
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • 9367129
    • Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 1997, 13(5):555-556. 9367129
    • (1997) Comput Appl Biosci , vol.13 , Issue.5 , pp. 555-556
    • Yang, Z.1


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