메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Comparison of RefSeq protein-coding regions in human and vertebrate genomes

Author keywords

Genome annotation; Protein quality assessment; RefSeq proteins; Splice orthologs

Indexed keywords

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; EXON; GENE LOCATION; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; HUMAN GENOME; HUMAN VERSUS ANIMAL COMPARISON; MAMMALIAN GENETICS; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PROTEIN DOMAIN; PROTEIN PROCESSING; REFERENCE DATABASE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; ANIMAL; COMPARATIVE STUDY; GENETIC DATABASE; GENETICS; GENOME; HUMAN; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; OPEN READING FRAME; PROTEIN TERTIARY STRUCTURE; RNA SPLICING; SPECIES DIFFERENCE; VERTEBRATE;

EID: 84884521241     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-654     Document Type: Article
Times cited : (13)

References (31)
  • 1
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
    • 0(Database issue)
    • Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 2012, 0(Database issue):D130-D135.
    • (2012) Nucleic Acids Res
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 2
    • 67650064594 scopus 로고    scopus 로고
    • The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes
    • 10.1101/gr.080531.108, 2704439, 19498102
    • Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, et al. The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 2009, 19(7):1316-1323. 10.1101/gr.080531.108, 2704439, 19498102.
    • (2009) Genome Res , vol.19 , Issue.7 , pp. 1316-1323
    • Pruitt, K.D.1    Harrow, J.2    Harte, R.A.3    Wallin, C.4    Diekhans, M.5    Maglott, D.R.6    Searle, S.7    Farrell, C.M.8    Loveland, J.E.9    Ruef, B.J.10
  • 4
    • 74549221383 scopus 로고    scopus 로고
    • Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
    • 10.1371/journal.pcbi.1000605, 2781113, 20011109
    • Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 2009, 5(12):e1000605. 10.1371/journal.pcbi.1000605, 2781113, 20011109.
    • (2009) PLoS Comput Biol , vol.5 , Issue.12
    • Schnoes, A.M.1    Brown, S.D.2    Dodevski, I.3    Babbitt, P.C.4
  • 5
    • 43249097469 scopus 로고    scopus 로고
    • Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes
    • 10.1371/journal.pcbi.1000067, 2291194, 18421375
    • Lin MF, Deoras AN, Rasmussen MD, Kellis M. Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PLoS Comput Biol 2008, 4(4):e1000067. 10.1371/journal.pcbi.1000067, 2291194, 18421375.
    • (2008) PLoS Comput Biol , vol.4 , Issue.4
    • Lin, M.F.1    Deoras, A.N.2    Rasmussen, M.D.3    Kellis, M.4
  • 7
    • 84855327164 scopus 로고    scopus 로고
    • Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons
    • 10.1101/gr.119834.110, 3246205, 21974994
    • Gelfman S, Burstein D, Penn O, Savchenko A, Amit M, Schwartz S, Pupko T, Ast G. Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res 2012, 22(1):35-50. 10.1101/gr.119834.110, 3246205, 21974994.
    • (2012) Genome Res , vol.22 , Issue.1 , pp. 35-50
    • Gelfman, S.1    Burstein, D.2    Penn, O.3    Savchenko, A.4    Amit, M.5    Schwartz, S.6    Pupko, T.7    Ast, G.8
  • 9
    • 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
  • 10
    • 0033861549 scopus 로고    scopus 로고
    • Human and mouse gene structure: comparative analysis and application to exon prediction
    • 10.1101/gr.10.7.950, 310911, 10899144
    • Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res 2000, 10(7):950-958. 10.1101/gr.10.7.950, 310911, 10899144.
    • (2000) Genome Res , vol.10 , Issue.7 , pp. 950-958
    • Batzoglou, S.1    Pachter, L.2    Mesirov, J.P.3    Berger, B.4    Lander, E.S.5
  • 11
    • 84859619817 scopus 로고    scopus 로고
    • The ancient and evolving roles of cohesin in gene expression and DNA repair
    • 10.1016/j.cub.2012.02.046, 3327610, 22497943
    • Dorsett D, Strom L. The ancient and evolving roles of cohesin in gene expression and DNA repair. Curr Biol 2012, 22(7):R240-R250. 10.1016/j.cub.2012.02.046, 3327610, 22497943.
    • (2012) Curr Biol , vol.22 , Issue.7
    • Dorsett, D.1    Strom, L.2
  • 12
    • 33646346868 scopus 로고    scopus 로고
    • The essential vertebrate ABCE1 protein interacts with eukaryotic initiation factors
    • 10.1074/jbc.M510603200, 16421098
    • Chen ZQ, Dong J, Ishimura A, Daar I, Hinnebusch AG, Dean M. The essential vertebrate ABCE1 protein interacts with eukaryotic initiation factors. J Biol Chem 2006, 281(11):7452-7457. 10.1074/jbc.M510603200, 16421098.
    • (2006) J Biol Chem , vol.281 , Issue.11 , pp. 7452-7457
    • Chen, Z.Q.1    Dong, J.2    Ishimura, A.3    Daar, I.4    Hinnebusch, A.G.5    Dean, M.6
  • 14
    • 80052848466 scopus 로고    scopus 로고
    • Computational methods for Gene Orthology inference
    • 10.1093/bib/bbr030, 3178053, 21690100
    • Kristensen DM, Wolf YI, Mushegian AR, Koonin EV. Computational methods for Gene Orthology inference. Brief Bioinform 2011, 12(5):379-391. 10.1093/bib/bbr030, 3178053, 21690100.
    • (2011) Brief Bioinform , vol.12 , Issue.5 , pp. 379-391
    • Kristensen, D.M.1    Wolf, Y.I.2    Mushegian, A.R.3    Koonin, E.V.4
  • 16
    • 59149102602 scopus 로고    scopus 로고
    • Phylogenetic and functional assessment of orthologs inference projects and methods
    • 10.1371/journal.pcbi.1000262, 2612752, 19148271
    • Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 2009, 5(1):e1000262. 10.1371/journal.pcbi.1000262, 2612752, 19148271.
    • (2009) PLoS Comput Biol , vol.5 , Issue.1
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 17
    • 46649115430 scopus 로고    scopus 로고
    • Splign: algorithms for computing spliced alignments with identification of paralogs
    • 10.1186/1745-6150-3-20, 2440734, 18495041
    • Kapustin Y, Souvorov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol Direct 2008, 3:20. 10.1186/1745-6150-3-20, 2440734, 18495041.
    • (2008) Biol Direct , vol.3 , pp. 20
    • Kapustin, Y.1    Souvorov, A.2    Tatusova, T.3    Lipman, D.4
  • 18
    • 36549051577 scopus 로고    scopus 로고
    • Aligning multiple whole genomes with Mercator and MAVID
    • 10.1007/978-1-59745-514-5_14, 17993677
    • Dewey CN. Aligning multiple whole genomes with Mercator and MAVID. Methods Mol Biol 2007, 395:221-236. 10.1007/978-1-59745-514-5_14, 17993677.
    • (2007) Methods Mol Biol , vol.395 , pp. 221-236
    • Dewey, C.N.1
  • 19
    • 43349098885 scopus 로고    scopus 로고
    • Exalign: a new method for comparative analysis of exon-intron gene structures
    • 10.1093/nar/gkn153, 2377436, 18397951
    • Pavesi G, Zambelli F, Caggese C, Pesole G. Exalign: a new method for comparative analysis of exon-intron gene structures. Nucleic Acids Res 2008, 36(8):e47. 10.1093/nar/gkn153, 2377436, 18397951.
    • (2008) Nucleic Acids Res , vol.36 , Issue.8
    • Pavesi, G.1    Zambelli, F.2    Caggese, C.3    Pesole, G.4
  • 20
    • 79961109822 scopus 로고    scopus 로고
    • Domain architecture conservation in orthologs
    • 10.1186/1471-2105-12-326, 3215765, 21819573
    • Forslund K, Pekkari I, Sonnhammer EL. Domain architecture conservation in orthologs. BMC Bioinformatics 2011, 12:326. 10.1186/1471-2105-12-326, 3215765, 21819573.
    • (2011) BMC Bioinformatics , vol.12 , pp. 326
    • Forslund, K.1    Pekkari, I.2    Sonnhammer, E.L.3
  • 21
    • 34250333457 scopus 로고    scopus 로고
    • Domain architecture comparison for multidomain homology identification
    • 10.1089/cmb.2007.A009, 17572026
    • Song N, Sedgewick RD, Durand D. Domain architecture comparison for multidomain homology identification. J Comput Biol 2007, 14(4):496-516. 10.1089/cmb.2007.A009, 17572026.
    • (2007) J Comput Biol , vol.14 , Issue.4 , pp. 496-516
    • Song, N.1    Sedgewick, R.D.2    Durand, D.3
  • 22
    • 79551487629 scopus 로고    scopus 로고
    • Alternative translation start sites are conserved in eukaryotic genomes
    • 10.1093/nar/gkq806, 3025576, 20864444
    • Bazykin GA, Kochetov AV. Alternative translation start sites are conserved in eukaryotic genomes. Nucleic Acids Res 2011, 39(2):567-577. 10.1093/nar/gkq806, 3025576, 20864444.
    • (2011) Nucleic Acids Res , vol.39 , Issue.2 , pp. 567-577
    • Bazykin, G.A.1    Kochetov, A.V.2
  • 23
    • 84861549132 scopus 로고    scopus 로고
    • Limitations of the rhesus macaque draft genome assembly and annotation
    • 10.1186/1471-2164-13-206, 3426473, 22646658
    • Zhang X, Goodsell J, Norgren RB. Limitations of the rhesus macaque draft genome assembly and annotation. BMC Genomics 2012, 13:206. 10.1186/1471-2164-13-206, 3426473, 22646658.
    • (2012) BMC Genomics , vol.13 , pp. 206
    • Zhang, X.1    Goodsell, J.2    Norgren, R.B.3
  • 24
    • 79955684513 scopus 로고    scopus 로고
    • Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation
    • 10.1371/journal.pone.0018910, 3083393, 21556138
    • Chen C, Natale DA, Finn RD, Huang H, Zhang J, Wu CH, Mazumder R. Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One 2011, 6(4):e18910. 10.1371/journal.pone.0018910, 3083393, 21556138.
    • (2011) PLoS One , vol.6 , Issue.4
    • Chen, C.1    Natale, D.A.2    Finn, R.D.3    Huang, H.4    Zhang, J.5    Wu, C.H.6    Mazumder, R.7
  • 25
    • 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
  • 27
    • 3242887157 scopus 로고    scopus 로고
    • CD-Search: protein domain annotations on the fly
    • (Web Server issue)
    • Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res 2004, 32(Web Server issue):W327-W331.
    • (2004) Nucleic Acids Res , vol.32
    • Marchler-Bauer, A.1    Bryant, S.H.2
  • 28
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: discriminating signal peptides from transmembrane regions
    • 10.1038/nmeth.1701, 21959131
    • Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8(10):785-786. 10.1038/nmeth.1701, 21959131.
    • (2011) Nat Methods , vol.8 , Issue.10 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    von Heijne, G.3    Nielsen, H.4
  • 29
    • 34249857539 scopus 로고    scopus 로고
    • COBALT: constraint-based alignment tool for multiple protein sequences
    • 10.1093/bioinformatics/btm076, 17332019
    • Papadopoulos JS, Agarwala R. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 2007, 23(9):1073-1079. 10.1093/bioinformatics/btm076, 17332019.
    • (2007) Bioinformatics , vol.23 , Issue.9 , pp. 1073-1079
    • Papadopoulos, J.S.1    Agarwala, R.2
  • 30
    • 84886369967 scopus 로고    scopus 로고
    • NCBI web site http://www.ncbi.nlm.nih.gov.
    • NCBI web site


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.