Genomewide function conservation and phylogeny in the herpesviridae

被引:59
作者
Albà, MM
Das, RJ
Orengo, CA
Kellam, P [1 ]
机构
[1] UCL, Dept Immunol & Mol Pathol, Wohl Virion Ctr, London W1T 4JF, England
[2] UCL, Ctr Math & Phys Sci Appl Life Sci & Expt Biol, London W1T 4JF, England
[3] UCL, Dept Biochem, Biomol Struct & Modeling Unit, London W1T 4JF, England
关键词
D O I
10.1101/gr.149801
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The Herpesviridae are a large group of well-characterized double-stranded DNA viruses for which many complete genome sequences have been determined. We have extracted protein sequences from all predicted open reading frames of 19 herpesvirus genomes. Sequence comparison and protein sequence clustering methods have been used to construct herpesvirus protein homologous families. This resulted in 1692 proteins being clustered into 243 multiprotein families and 196 singleton proteins. Predicted functions were assigned to each homologous family based on genome annotation and published data and each family classified into seven broad functional groups. Phylogenetic profiles were constructed for each herpesvirus from the homologous protein families and used to determine conserved functions and genomewide phylogenetic trees. These trees agreed with molecular-sequence-derived trees and allowed greater insight into the phylogeny of ungulate and murine gammaherpesviruses.
引用
收藏
页码:43 / 54
页数:12
相关论文
共 26 条
  • [1] ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999
  • [2] Functional classes in the three domains of life
    Andrade, MA
    Ouzounis, C
    Sander, C
    Tamames, J
    Valencia, A
    [J]. JOURNAL OF MOLECULAR EVOLUTION, 1999, 49 (05) : 551 - 557
  • [3] AMINO-ACID SUBSTITUTION DURING FUNCTIONALLY CONSTRAINED DIVERGENT EVOLUTION OF PROTEIN SEQUENCES
    BENNER, SA
    COHEN, MA
    GONNET, GH
    [J]. PROTEIN ENGINEERING, 1994, 7 (11): : 1323 - 1332
  • [4] GenBank
    Benson, DA
    Boguski, MS
    Lipman, DJ
    Ostell, J
    Ouellette, BFF
    Rapp, BA
    Wheeler, DL
    [J]. NUCLEIC ACIDS RESEARCH, 1999, 27 (01) : 12 - 17
  • [5] Human cytomegalovirus clinical isolates carry at least 19 genes not found in laboratory strains
    Cha, TA
    Tom, E
    Kemble, GW
    Duke, GM
    Mocarski, ES
    Spaete, RR
    [J]. JOURNAL OF VIROLOGY, 1996, 70 (01) : 78 - 83
  • [6] Felsenstein J., 1993, PHYLIP PHYLOGENY INF
  • [7] Whole genome-based phylogenetic analysis of free-living microorganisms
    Fitz-Gibbon, ST
    House, CH
    [J]. NUCLEIC ACIDS RESEARCH, 1999, 27 (21) : 4218 - 4222
  • [8] Gouzy J, 1997, COMPUT APPL BIOSCI, V13, P601
  • [9] Whole genome protein domain analysis using a new method for domain clustering
    Gouzy, J
    Corpet, F
    Kahn, D
    [J]. COMPUTERS & CHEMISTRY, 1999, 23 (3-4): : 333 - 340
  • [10] GENOME SEQUENCE COMPARISON AND SCENARIOS FOR GENE REARRANGEMENTS - A TEST-CASE
    HANNENHALLI, S
    CHAPPEY, C
    KOONIN, EV
    PEVZNER, PA
    [J]. GENOMICS, 1995, 30 (02) : 299 - 311