Comparative DNA analysis across diverse genomes

被引：256

作者：

Karlin, S ^{[1
]}

Campbell, AM

Mrázek, J

机构：

[1] Stanford Univ, Dept Math, Stanford, CA 94305 USA

[2] Stanford Univ, Dept Biol Sci, Stanford, CA 94305 USA

来源：

ANNUAL REVIEW OF GENETICS | 1998年 / 32卷

关键词：

genome signature; compositional biases; frequent oligonucleotides (motifs); strand compositional asymmetry; codon biases;

D O I：

10.1146/annurev.genet.32.1.185

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

We review concepts and methods for comparative analysis of complete genomes including assessments of genomic compositional contrasts based on dinucleotide and tetranucleotide relative abundance values, identifications of rare and frequent oligonucleotides, evaluations and interpretations of codon biases in several large prokaryotic genomes, and characterizations of compositional asymmetry between the two DNA strands in certain bacterial genomes. The discussion also covers means for identifying alien (e.g. laterally transferred) genes and detecting potential specialization islands in bacterial genomes.

引用

页码：185 / 225

页数：41

共 93 条

[21] Calladine CR., 1992, Understanding DNA
[22] PERVASIVE CPG SUPPRESSION IN ANIMAL MITOCHONDRIAL GENOMES
CARDON, LR
BURGE, C
CLAYTON, DA
KARLIN, S
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (09) : 3799 - 3803
[23] Did the inheritance of a pathogenicity island modify the virulence of Helicobacter pylori?
Covacci, A
Falkow, S
Berg, DE
Rappuoli, R
[J]. TRENDS IN MICROBIOLOGY, 1997, 5 (05) : 205 - 208
[24] DELCOURT SG, 1991, J BIOL CHEM, V266, P15160
[25] DNA METHYLATION AND GENE ACTIVITY
DOERFLER, W
[J]. ANNUAL REVIEW OF BIOCHEMISTRY, 1983, 52 : 93 - 124
[26] ECHOLS H, 1991, ANNU REV BIOCHEM, V60, P477, DOI 10.1146/annurev.biochem.60.1.477
[27] BASE COMPOSITIONAL STRUCTURE OF GENOMES
FICKETT, JW
TORNEY, DC
WOLF, DR
[J]. GENOMICS, 1992, 13 (04) : 1056 - 1064
[28] RECOGNITION OF PROTEIN CODING REGIONS IN DNA-SEQUENCES
FICKETT, JW
[J]. NUCLEIC ACIDS RESEARCH, 1982, 10 (17) : 5303 - 5318
[29] Common themes in microbial pathogenicity revisited
Finlay, BB
Falkow, S
[J]. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 1997, 61 (02) : 136 - +
[30] Strand asymmetries in DNA evolution
Francino, MP
Ochman, H
[J]. TRENDS IN GENETICS, 1997, 13 (06) : 240 - 245

← 1 2 3 4 5 6 7 8 9 10 →