GenomeHistory: A software tool and its application to fully sequenced genomes

Nucleic Acids Research

Volumn 30, Issue 15, 2002, Pages 3378-3386

  Conant, Gavin C ^a   Wagner, Andreas ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; DROSOPHILA; ESCHERICHIA COLI; EUKARYOTE; GENE DUPLICATION; GENE FUNCTION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; INTERNET; MULTIGENE FAMILY; NEMATODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROKARYOTE; RIBOSOME; SEQUENCE ANALYSIS; YEAST;

DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; EUKARYOTA; NEGIBACTERIA; NEMATODA; PROKARYOTA; SACCHAROMYCETALES;

EID: 0036682357     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf449     Document Type: Article

References (45)

1. Evolution by Gene Duplication
2. Evolution of gene families and relationship with organismal evolution: Rapid divergence of tissue-specific genes in the early evolution of chordates
3. Gene duplications in early metazoan evolution
4. Rate of gene silencing at duplicate loci: A theoretical study and interpretation of data from tetraploid fish
5. Probability of fixation of nonfunctional genes at duplicate loci
6. Evolution of the differential regulation of duplicate genes after polyploidization
7. Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution
8. Preservation of duplicate genes by complementary, degenerative mutations
9. Molecular evidence for an ancient duplication of the entire yeast genome
10. Extent of genomic rearrangement after genome duplication in yeast
11. Digging for dead genes: An analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome
12. The evolutionary fate and consequences of duplicate genes
13. A structural census of genomes: Comparing bacterial, eukaryotic and archaeal genomes in terms of protein structure
14. The frequency distribution of gene family sizes in complete genomes
15. Protein family and fold occurence in genomes: Power-law behavior and evolutionary model
16. Comparative genomics of the eukaryotes
17. Comparison of the complete protein sets of worm and yeast: Orthology and divergence
18. Selection in the evolution of gene duplicates
19. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
20. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
21. Life with 6000 genes
22. The genome sequence of Schizosaccharomyces pombe
23. The genome sequence of Drosophila melanogaster
24. Genome sequence of the nematode C. elegans: A platform for investigating biology
25. The complete genome sequence of Escherichia coli K-12
26. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
27. A codon-based model of nucleotide substitution for protein-coding DNA sequences
28. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
29. Numerical Recipes in C
30. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A
31. Gene ontology: Tool for the unification of biology
32. Basic local alignment search tool
33. The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae
34. Multiple duplications of yeast hexose-transport genes in response to selection in a glucose-limited environment
35. The yeast protein interaction network evolves rapidly and contains few duplicate genes
36. Extensive gene duplication in the early evolution of animals before the parazoan-eumetazoan split demonstrated by G proteins and protein tyrosine kinases from sponge and hydra
37. Molecular characterization of the histone gene family of Caenorhabditis elegans
38. Seripauperins of Saccharomyces cerevisiae: A new multigene family encoding serine-poor relatives of serine-rich proteins
39. The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene function
40. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
41. Robustness against mutations in genetic networks of yeast
42. Isolation and characterization of a sperm-specific gene family in the nematode Caenorhabditis elegans
43. Acting like actin: The dynamics of the nematode major sperm protein (MSP) cytoskeleton indicate a push-pull mechanism for amoeboid cell motility
44. A sperm cytoskeletal protein that signals oocyte meiotic maturation and ovulation