Comparative genomics

Annual Review of Genomics and Human Genetics

Volumn 5, Issue , 2004, Pages 15-56

  Miller, Webb ^a   Makova, Kateryna D ^a   Nekrutenko, Anton ^a   Hardison, Ross C ^a  

^a NONE

Author keywords

Bioinformatics; Evolutionary rates; Gene prediction; Gene regulation; Genome browsers; Genome databases; Internet resources; Sequence conservation; Whole genome alignments

Indexed keywords

BIOINFORMATICS; EVOLUTION; GENE CONTROL; GENE FUNCTION; GENE SEQUENCE; GENETIC SELECTION; GENOME; GENOMICS; HUMAN; MAMMAL; MOUSE; NONHUMAN; RAT; REVIEW; SYSTEMATIC REVIEW; WORM; YEAST;

ANIMALS; CAENORHABDITIS; EVOLUTION; GENOMICS; HUMANS; MICE; RATS; YEASTS;

MAMMALIA;

EID: 5444257222     PISSN: 15278204     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genom.5.061903.180057     Document Type: Review

References (193)

1. Alexandersson M, Cawley S, Pachter L. 2003. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome. Res. 13:496-502
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-10
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:3389-402
4. Ansari-Lari MA, Oeltjen JC, Schwartz S, Zhang Z, Muzny DM, et al. 1998. Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome. Res. 8:29-40
5. Antequera FB, Bird A. 1993. Number of CpG islands and genes in human and mouse. Proc. Natl. Acad. Sci. USA 90:11995-99
6. Aparicio S, Morrison A, Gould A, Gilthorpe J, Chaudhuri C, et al. 1995. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl. Acad. Sci. USA 92:1684-88
7. Armengol L, Pujana MA, Cheung J, Scherer SW, Estivill X. 2003. Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum. Mol. Genet. 12:2201-8
8. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. 2000. Gene ontology: tool for the unification of biology. Nat. Genet. 25:25-29
9. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, et al. 2002. Recent segmental duplications in the human genome. Science 297:1003-7
10. Bailey JA, Yavor AM, Viggiano L, Misceo D, Horvath JE, et al. 2002. Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70:83-100
11. Bailey TL, Elkan C. 1995. The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3:21-29
12. Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. 2000. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome. Res. 10:950-58
13. Begun DJ, Aquadro CF. 1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356:519-20
14. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, et al. 2002. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. USA 99:757-62
15. Bernardi G. 1995. The human genome: organization and evolutionary history. Annu. Rev. Genet. 29:445-76
16. Bird AP. 1986. CpG-rich islands and the function of DNA methylation. Nature 321:209-13
17. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome. Res. 14:708-15
18. Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, et al. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299:1391-94
19. Bray N, Dubchak I, Pachter L. 2003. AVID: A global alignment program. Genome. Res. 13:97-102
20. Bray N, Pachter L. 2003. MAVID multiple alignment server. Nucl. Acids Res. 31:3525-26
21. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, et al. 2003. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome. Res. 13:721-31
22. Bulger M, Bender MA, von Doorninck JH, Wertman B, Farrell C, et al. 2000. Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse β-globin gene clusters. Proc. Natl. Acad. Sci. USA 97:14560-65
23. Burge C. 1997. Identification of genes in human genomic DNA. PhD thesis. Stanford Univ., Stanford, Calif.
24. Burge C, Karlin S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:78-94
25. C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012-18
26. Castresana J. 2002. Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content. Nucl. Acids Res. 30:1751-56
27. Chapman MA, Charchar FJ, Kinston S, Bird CP, Grafham D, et al. 2003. Comparative and functional analyses of LYL1 loci establish marsupial sequences as a model for phylogenetic footprinting. Genomics 81:249-59
28. Cheung J, Wilson MD, Zhang J, Khaja R, MacDonald JR, et al. 2003. Recent segmental and gene duplications in the mouse genome. Genome. Biol. 4:R47
29. Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, et al. 2001. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409:953-58
30. Chiaromonte F, Yang S, Elnitski L, Yap V, Miller W, Hardison RC. 2001. Association between divergence and interspersed repeats in mammalian non-coding genomic DNA. Proc. Natl. Acad. Sci. USA 98:14503-8
31. Chuang J, Li H. 2004. Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. Public Libr. Sci. Biol. 2:253-63.
32. Clamp M, Andrews D, Barker D, Bevan P, Cameron G, et al. 2003. Ensembl 2002: accommodating comparative genomics. Nucl. Acids Res. 31:38-42
33. Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, et al. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76
34. Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, et al. 2001. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome. Res. 11:1175-86
35. Collins FS, Green ED, Guttmacher AE, Guyer MS. 2003. A vision for the future of genomics research. Nature 422:835-47
36. Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, et al. 2003. Strategies and tools for whole-genome alignments. Genome. Res. 13:73-80
37. Crollius HR, Jaillon O, Bernot A, Dasilva C, Bouneau L, et al. 2000. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat. Genet. 25:235-38
38. Dermitzakis E, Clark A. 2002. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 19:1114-21
39. Dermitzakis ET, Reymond A, Scamuffa N, Ucla C, Kirkness E, et al. 2003. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science 302:1033-35
40. DeSilva U, Elnitski L, Idol JR, Doyle JL, Gan W, et al. 2002. Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome. Genome. Res. 12:3-15
41. Dieterich C, Wang H, Rateitschak K, Luz H, Vingron M. 2003. CORG: a database for comparative regulatory genomics. Nucl. Acids Res. 31:55-57
42. Dubchak I, Pachter L. 2002. The computational challenges of applying comparative-based computational methods to whole genomes. Brief Bioinform. 3:18-22
43. Easteal S, Collet C. 1994. Consistent variation in amino-acid substitution rate, despite uniformity of mutation rate: protein evolution in mammals is not neutral. Mol. Biol. Evol. 11:643-17
44. Efstratiadis A, Posakony JW, Maniatis T, Lawn RM, O'Connell C, et al. 1980. The structure and evolution of the human β-globin gene family. Cell 21:653-68
45. Ellegren H, Smith NG, Webster MT. 2003. Mutation rate variation in the mammalian genome. Curr. Opin. Genet. Dev. 13:562-68
46. Ellsworth RE, Jamison DC, Touchman JW, Chissoe SL, Braden Maduro VV, et al. 2000. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes. Proc. Natl. Acad. Sci. USA 97:1172-77
47. Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, et al. 2003. Distinguishing regulatory DNA from neutral sites. Genome. Res. 13:64-72
48. Elnitski L, Miller W, Hardison R. 1997. Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the β-globin locus control region: role of basic helix-loop-helix proteins. J. Biol. Chem. 272:369-78
49. Emorine L, Kuehl M, Weir L, Leder P, Max EE. 1983. A conserved sequence in the immunoglobulin JK-CK intron: possible enhancer element. Nature 304:447-19
50. Endrizzi M, Huang S, Scharf JM, Kelter AR, Wirth B, et al. 1999. Comparative sequence analysis of the mouse and human Lgn1/SMA interval. Genomics 60:137-51
51. Epp TA, Wang R, Sole MJ, Liew CC. 1995. Concerted evolution of mammalian cardiac myosin heavy chain genes. J. Mol. Evol. 41:284-92
52. Eyre-Walker A. 1999. Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics 152:675-83
53. Fickett JW, Tung CS. 1992. Assessment of protein coding measures. Nucl. Acids Res. 20:6441-50
54. Flint J, Tufarelli C, Peden J, Clark K, Daniels RJ, et al. 2001. Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster. Hum. Mol. Genet. 10:371-82
55. Florea L, Li M, Riemer C, Giardine B, Miller W, Hardison R. 2000. Validating computer programs for functional genomics in gene regulatory regions. Curr. Genom. 1:11-27
56. Fortna A, Gardiner K. 2001. Genomic sequence analysis tools: a user's guide. Trends Genet. 17:158-64
57. Frazer KA, Elnitski L, Church D, Dubchak I, Hardison RC. 2003. Cross-species sequence comparisons: a review of methods and available resources. Genome. Res. 13:1-12
58. Fullerton SM, Bond J, Schneider JA, Hamilton B, Harding RM, et al. 2000. Polymorphism and divergence in the beta-globin replication origin initiation region. Mol. Biol. Evol. 17:179-88
59. Fullerton SM, Carvalho AB, Clark AG. 2001. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18:1139-42
60. Giardine BM, Elnitski L, Riemer C, Makalowska I, Schwartz S, et al. 2003. GALA, a database for genomic sequence alignments and annotations. Genome. Res. 13:732-41
61. Goodman M. 1961. The role of immunochemical differences in the phyletic development of human behavior. Hum. Biol. 33:131-62
62. Goodman M, Barnabas J, Matsuda G, Moore GW. 1971. Molecular evolution in the descent of man. Nature 233:604-13
63. Gottgens B, Barton LM, Gilbert JG, Bench AJ, Sanchez MJ, et al. 2000. Analysis of vertebrate SCL loci identifies conserved enhancers. Nat. Biotechnol. 18:181-86
64. Gottgens B, Gilbert JG, Barton LM, Grafham D, Rogers J, et al. 2001. Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved non-coding sequences. Genome. Res. 11:87-97
65. Graur D. 1985. Amino acid composition and the evolutionary rates of protein-coding genes. J. Mol. Evol. 22:53-62
66. Gregory TR. 2003. Is small indel bias a determinant of genome size? Trends Genet. 19:485-88
67. Grosveld F, van Assendelft GB, Greaves D, Kollias G. 1987. Position-independent, high-level expression of the human β-globin gene in transgenic mice. Cell 51:975-85
68. Guigo R. 1998. Assembling genes from predicted exons in linear time with dynamic programming. J. Comput. Biol. 5:681-702
69. Guigo R, Agarwal P, Abril JF, Burset M, Fickett JW. 2000. An assessment of gene prediction accuracy in large DNA sequences. Genome. Res. 10:1631-42
70. Gumucio D, Shelton D, Zhu W, Millinoff D, Gray T, et al. 1996. Evolutionary strategies for the elucidation of cis and trans factors that regulate the developmental switching programs of the beta-like globin genes. Mol. Phylogent. Evol. 5:18-32
71. Gumucio DL, Blanchard-McQuate KL, Heilstedt-Williamson H, Tagle D, Gray TA, et al. 1991. γ-Globin gene regulation: evolutionary approaches. In The Regulation of Hemoglobin Switching, ed. G Stamatoyannopoulos, AW Nienhuis, pp. 277-89. Baltimore, MD: Johns Hopkins Univ. Press
72. Gumucio DL, Heilstedt-Williamson H, Gray TA, Tarle SA, Shelton DA, et al. 1992. Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human γ and ε globin genes. Mol. Cell. Biol. 12:4919-29
73. Gumucio DL, Shelton DA, Bailey WJ, Slightom JL, Goodman M. 1993. Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the ε-globin gene. Proc. Natl. Acad. Sci. USA 90:6018-22
74. Hardison R, Krane D, Vandenbergh D, Cheng J-F, Mansberger J, et al. 1991. Sequence and comparative analysis of the rabbit α-like globin gene cluster reveals a rapid mode of evolution in a G+C rich region of mammalian genomes. J. Mol. Biol. 222:233-49
75. Hardison R, Oeltjen J, Miller W. 1997. Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome. Res. 7:959-66
76. Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, et al. 2004. Global predictions and tests of erythroid regulatory regions. In The Genome of Homo sapiens. Cold Spring Harbor, NY: Cold Spring Harbor
77. Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, et al. 2003. Co-variation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution. Genome. Res. 13:13-26
78. Hein J. 1989. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol. Biol. Evol. 6:649-68
79. Hellmann I, Ebersberger I, Ptak SE, Paabo S, Przeworski M. 2003. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72:1527-35
80. Higgs D, Wood W, Jarman A, Sharpe J, Lida J, et al. 1990. A major positive regulatory region located far upstream of the human α-globin gene locus. Genes Dev. 4:1588-601
81. Huang X, Pevzner P, Miller W. 1994. Parametric recomputing in alignment graphs. In Combinatorial Pattern Matching, pp. 87-101. Springer Lecture Notes in Computer Science, 807. Springer-Verlag
82. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, et al. 2002. The Ensembl genome database project. Nucl. Acids Res. 30:38-41
83. Hughes AL, Nei M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-70
84. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
85. Jane SM, Ney PA, Vanin EF, Gumucio DL, Nienhuis AW. 1992. Identification of a stage selector element in the human γ-globin gene promoter that fosters preferential interaction with the 5′ HS2 enhancer when in competition with the β-promoter. EMBO J. 11:2961-69
86. Jordan IK, Rogozin IB, Glazko GV, Koonin EV. 2003. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 19:68-72
87. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, et al. 2003. The UCSC Genome Browser Database. Nucl. Acids Res. 31:51-54
88. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, et al. 2004. The UCSC Table Browser data retrieval tool. Nucl. Acids Res. 32:D493-96
89. Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, et al. 2003. EnsMart-a generic system for fast and flexible access to biological data. Genome Res. 14:160-69
90. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-54
91. Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome. Res. 12:656-64
92. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. 2003. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. USA 100:11484-89
93. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. 2002. The human genome browser at UCSC. Genome. Res. 12:996-1006
94. Kimura M. 1968. Evolutionary rate at the molecular level. Nature 217:624-26
95. Kimura M. 1977. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267:275-76
96. Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, et al. 2003. The dog genome: survey sequencing and comparative analysis. Science 301:1898-903
97. Kohne DE. 1970. Evolution of higher-organism DNA. Q. Rev. Biophys. 3:327-75
98. Koop BF. 1995. Human and rodent sequence comparisons: a mosaic model of genomic evolution. Trends Genet. 11:367-71
99. Koop BF, Hood L. 1994. Striking sequence similarity over almost 100 kilo-bases of human and mouse T-cell receptor DNA. Nat. Genet. 7:48-53
100. Korf I, Flicek P, Duan D, Brent MR. 2001. Integrating genomic homology into gene structure prediction. Bioinformatics 17 Suppl 1:S140-48
101. Krawczak M, Ball EV, Cooper DN. 1998. Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. Am. J. Hum. Genet. 63:474-88
102. Lamerdin JE, Montgomery MA, Stilwagen SA, Scheidecker LK, Tebbs RS, et al. 1995. Genomic sequence comparison of the human and mouse XRCC1 DNA repair gene regions. Genomics 25:547-54
103. Lamerdin JE, Stilwagen SA, Ramirez MH, Stubbs L, Carrano AV. 1996. Sequence analysis of the ERCC2 gene regions in human, mouse, and hamster reveals three linked genes. Genomics 34:399-109
104. Lee C, Grasso C, Sharlow MF. 2002. Multiple sequence alignment using partial order graphs. Bioinformatlcs 18:452-64
105. Lee YH, Ota T, Vacquier VD. 1995. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Mol. Biol. Evol. 12:231-38
106. Lercher MJ, Hurst LD. 2002. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18:337-10
107. Lercher MJ, Urrutia AO, Hurst LD. 2002. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31:180-83
108. Li J, Miller W. 2003. Significance of interspecies matches when evolutionary rate varies. J. Comput. Biol. 10:537-54
109. Li W-H. 1997. Molecular Evolution. Sunderland, MA: Sinauer
110. Li W-H, Gouy M, Sharp P, O'hUigin C, Yang Y-W. 1990. Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla and carnivora and molecular clocks. Proc. Natl. Acad. Sci. USA 87:6703-7
111. Li WH, Wu CI. 1987. Rates of nucleotide substitution are evidently higher in rodents than in man. Mol. Biol. Evol. 4:74-82
112. Li WH, Wu CI, Luo CC. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-74
113. Li WH, Yi S, Makova K. 2002. Male-driven evolution. Curr. Opin. Genet. Dev. 12:650-56
114. Loots GG, Locksley RM, Blankespoor CM, Wang ZE, Miller W, et al. 2000. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288:136-40
115. Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM. 2002. rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome. Res. 12:832-39
116. Ludwig MZ, Patel NH, Kreitman M. 1998. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 125:949-58
117. Lukashin AV, Borodovsky M. 1998. GeneMark.hmm: new solutions for gene finding. Nucl. Acids Res. 26:1107-15
118. Makalowski W, Boguski MS. 1998. Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. USA 95:9407-12
119. Makova K, Yang S, Chiaromonte F. 2004. Small indels are male-biased too: a whole-genome analysis in rodents. Genome. Res. 14:567-73
120. Makova KD, Ramsay M, Jenkins T, Li WH. 2001. Human DNA sequence variation in a 6.6-kb region containing the melanocortin 1 receptor promoter. Genetics 158:1253-68
121. Margot JB, Demers GW, Hardison RC. 1989. Complete nucleotide sequence of the rabbit β-like globin gene cluster: analysis of intergenic sequences and comparison with the human β-like globin gene cluster. J. Mol. Biol. 205:15-40
122. Margulies EH, Blanchette M, NISC Comparative Sequencing Program, Haussler D, Green ED. 2003. Identification and characterization of multispecies conserved sequences. Genome. Res. 13:2507-18
123. Matassi G, Sharp PM, Gautier C. 1999. Chromosomal location effects on gene sequence evolution in mammals. Curr. Biol. 9:786-91
124. Matsuo K, Clay O, Takahashi T, Silke J, Schaffner W. 1993. Evidence for erosion of mouse CpG islands during mammalian evolution. Somat. Cell Mol. Genet. 19:543-55
125. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, et al. 2000. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16:1046-47
126. McClelland M, Florea L, Sanderson K, Clifton SW, Parkhill J, et al. 2000. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucl. Acids Res. 28:4974-86
127. Messier W, Stewart CB. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385:151-54
128. Meyer IM, Durbin R. 2002. Comparative ab initio prediction of gene structures using pair HMMs. Bioinformatics 18:1309-18
129. Miller W. 2000. So many genomes, so little time. Nat. Biotechnol. 18:148-49
130. Miller W. 2001. Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics 17:391-97
131. Moss EG, Tang L. 2003. Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites. Dev. Biol. 258:432-42
132. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-62
133. Nachman MW. 2001. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17:481-85
134. Neafsey DE, Palumbi SR. 2003. Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes. Genome. Res. 13:821-30
135. Nei M. 1987. Molecular Evolutionary Genetics. New York: Columbia Univ. Press
136. Nekrutenko A, Chung WY, Li WH. 2003. ETOPE: Evolutionary test of predicted exons. Nucl. Acids Res. 31:3564-67
137. Nekrutenko A, Chung WY, Li WH. 2003. An evolutionary approach reveals a high protein-coding capacity of the human genome. Trends Genet. 19:306-10
138. Nekrutenko A, Makova KD, Li WH. 2002. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome. Res. 12:198-202
139. Nelson P, Kiriakidou M, Sharma A, Maniataki E, Mourelatos Z. 2003. The microRNA world: small is mighty. Trends Biochem. Sci. 28:534-40
140. Ning Z, Cox AJ, Mullikin JC. 2001. SSAHA: a fast search method for large DNA databases. Genome. Res. 11:1725-29
141. Oeltjen JC, Malley TM, Muzny DM, Miller W, Gibbs RA, Belmont JW. 1997. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome. Res. 7:315-29
142. Ovcharenko I, Loots GG, Hardison RC, Miller W, Stubbs L. 2004. zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. Genome. Res. 14:472-77
143. Pachter L, Alexandersson M, Cawley S. 2002. Applications of generalized pair hidden Markov models to alignment and gene finding problems. J. Comput. Biol. 9:389-99
144. Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigo R. 2003. Comparative gene prediction in human and mouse. Genome. Res. 13:108-17
145. Petrov DA, Sangster TA, Johnston JS, Hartl DL, Shaw KL. 2000. Evidence for DNA loss as a determinant of genome size. Science 287:1060-62
146. Pribnow D. 1975. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc. Natl. Acad. Sci. USA 72:784-88
147. Pruitt KD, Maglott DR. 2001. RefSeq and LocusLink: NCBI gene-centered resources. Nucl. Acids Res. 29:137-40
148. Rat Genome Sequencing Consortium. 2004. Evolution of the Mammalian Genome: sequence of the Genome of the Brown Norway Rat. Nature. 428:493-521
149. Reiser PJ, Kline WO. 1998. Electrophoretic separation and quantitation of cardiac myosin heavy chain isoforms in eight mammalian species. Am. J. Physiol. 274:H1048-53
150. Rogic S, Mackworth AK, Ouellette FB. 2001. Evaluation of gene-finding programs on mammalian sequences. Genome. Res. 11:817-32
151. Roskin K, Diekhans M, Haussler D. 2004. Score functions for assessing conservation in locally aligning regions of DNA from two species. J. Comput. Biol. In press
152. Rowitch DH, Echelard Y, Danielian PS, Gellner K, Brenner S, McMahon AP. 1998. Identification of an evolutionarily conserved 110 base-pair cis-acting regulatory sequence that governs Wnt-1 expression in the murine neural plate. Development 125:2735-46
153. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, et al. 2000. Comparative genomics of the eukaryotes. Science 287:2204-15
154. Saitoh N, Bell AC, Recillas-Targa F, West AG, Simpson M, et al. 2000. Structural and functional conservation at the boundaries of the chicken beta-globin domain. EMBO J. 19:2315-22
155. Salamov AA, Solovyev VV. 2000. Ab initio gene finding in Drosophila genomic DNA. Genome. Res. 10:516-22
156. Sarich VM, Wilson AC. 1967. Immunological time scale for hominid evolution. Science 158:1200-3
157. Schug J, Overton GC. 1997. Modeling transcription factor binding sites with Gibbs sampling and minimum description length encoding. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5:268-71
158. Schuler G, Epstein J, Ohkawa H, Kans J. 1996. Entrez: molecular biology database and retrieval system. Methods Enzymol. 266:141-62
159. Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, et al. 2003. MultiPip-Maker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucl. Acids Res. 31:3518-24
160. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, et al. 2003. Human-mouse alignments with Blastz. Genome. Res. 13:103-5
161. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, et al. 2000. PipMaker-a web server for aligning two genomic DNA sequences. Genome Res. 10:577-86
162. Shabalina SA, Ogurtsov AY, Kondrashov VA, Kondrashov AS. 2001. Selective constraint in intergenic regions of human and mouse genomes. Trends Genet. 17:373-76
163. Shehee R, Loeb DD, Adey NB, Burton FH, Casavant NC, et al. 1989. Nucleotide sequence of the BALB/c mouse β-globin complex. J. Mol. Biol. 205:41-62
164. Siepel A, Hausser D. 2004. Phylogenetic hidden Markov models. In Statistical Methods in Molecular Evolution, ed. R Nielsen. In press
165. Siepel A, Haussler D. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21:468-88
166. Smith NG, Webster MT, Ellegren H. 2002. Deterministic mutation rate variation in the human genome. Genome. Res. 12:1350-56
167. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, et al. 2003. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. Public Libr. Sci. Biol. 1:166-92
168. Stojanovic N, Florea L, Riemer C, Gumucio D, Slightom J, et al. 1999. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucl. Acids Res. 27:3899-910
169. Stoye J, Evers D, Meyer F. 1997. Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5:303-6
170. Stuart JM, Segal E, Koller D, Kim SK. 2003. A gene-coexpression network for global discovery of conserved genetic modules. Science 302:249-55
171. Su A, Cooke M, Ching K, Hakak Y, Walker J, et al. 2002. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. USA 99:4465-70
172. Sundstrom H, Webster MT, Ellegren H. 2003. Is the rate of insertion and deletion mutation male biased?: Molecular evolutionary analysis of avian and primate sex chromosome sequences. Genetics 164:259-68
173. Tagle DA, Koop BF, Goodman M, Slightom J, Hess DL, Jones RT. 1988. Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus): Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203:7469-80
174. Templeton AR, Clark AG, Weiss KM, Nickerson DA, Boerwinkle E, Sing CF. 2000. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am. J. Hum. Genet. 66:69-83
175. Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, et al. 2003. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424:788-93
176. Thompson W, Rouchka EC, Lawrence CE. 2003. Gibbs Recursive Sampler: finding transcription factor binding sites. Nucl. Acids Res 31:3580-85
177. Ting CT, Tsaur SC, Wu ML, Wu CI. 1998. A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 282:1501-4
178. Uberbacher EC, Mural RJ. 1991. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA 88:11261-65
179. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. 2001. The sequence of the human genome. Science 291:1304-51
180. Wasserman WW, Sandelin A. 2004. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5:276-87
181. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, et al. 2003. Database resources of the National Center for Biotechnology. Nucl. Acids Res. 31:28-33
182. Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, et al. 2002. Database resources of the National Center for Biotechnology Information: 2002 update. Nucl. Acids Res. 30:13-16
183. Wiehe T, Gebauer-Jung S, Mitchell-Olds T, Guigo R. 2001. SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome. Res. 11:1574-83
184. Wilson AC, Carlson SS, White TJ. 1977. Biochemical evolution. Annu. Rev. Biochem. 46:573-639
185. Wilson MD, Riemer C, Martindale DW, Schnupf P, Boright AP, et al. 2001. Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. Nucl. Acids Res. 29:1352-65
186. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, et al. 2001. The TRANSFAC system on gene expression regulation. Nucl. Acids Res. 29:281-83
187. Wolfe KH, Sharp PM, Li WH. 1989. Mutation rates differ among regions of the mammalian genome. Nature 337:283-85
188. Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, et al. 2004. Patterns of insertions and their covariation with substitutions in the rat, mouse and human genomes. Genome. Res. 14:517-27
189. Yi S, Ellsworth DL, Li WH. 2002. Slow molecular clocks in Old World monkeys, apes, and humans. Mol. Biol. Evol. 19:2191-98
190. Young JM, Trask BJ. 2002. The sense of smell: genomics of vertebrate odorant receptors. Hum. Mol. Genet. 11:1153-60
191. Zhang MQ. 2002. Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet. 3:698-709
192. Zhang P, Gu Z, Li WH. 2003. Different evolutionary patterns between young duplicate genes in the human genome. Genome. Biol. 4:R56
193. Zuckerkandl E, Pauling L. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8:357-66