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11.
Theoretical considerations have shown that the five possible overlapping
reading-frame configurations differ significantly in their coding
flexibility and thus in their information content (Siegel and Fitch 1980;
Smith and Waterman 1980). Contrary to expectation, the overlapping frame
configuration allowing the greatest coding flexibility is rarely seen,
whereas one of the most constraining is common. We point out here that this
overlapping reading-frame paradox and an observed but unexplained
preference in coding regions for a pyrimidine-purine at codon boundaries
(Shepherd 1981; Jones and Kafatos 1982; Smith et al. 1983) are intimately
linked. The codon boundary preference, which may be related to translation
efficiency or accuracy, places constraints on the evolution of overlapping
coding regions. These considerations may help identify actual coding
regions in DNA sequences. We have analyzed five sequenced (enteric)
bacterial insertion sequences for codon boundary incidences and
reading-frame configurations and find that they are consistent with these
proposed constraints.
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12.
Evolutionary relatedness of some primate models of Plasmodium 总被引:1,自引:0,他引:1
Primate--and, specifically, monkey--malaria infections are commonly used
for understanding the pathology of and immune response to the human disease
because they are thought to resemble most closely the host-parasite
relationship found in humans. Plasmodium cynomolgi is used extensively as a
model for the human parasite, P. vivax, and P. knowlesi is used primarily
as a model for the development of erythrocytic-stage vaccines. Both of
these simian parasites can naturally infect man, resulting in mildly
symptomatic episodes of the disease. The phylogenetic relationship between
these two simian parasites and previously characterized Plasmodium species,
including P. vivax, was examined by comparison of the asexually expressed
small- subunit ribosomal RNA genes. Our analysis confirmed that P. vivax is
most closely related to P. cynomolgi and that it remains an appropriate
model of the human pathogen. Furthermore, with P. knowlesi and P. fragile,
these two species form a group of closely related species, distant from
other Plasmodium species. What is considered to be the most ancient of the
human malaria pathogens, P. malariae, was also included in the analysis and
does not group at all with other simian or human parasites.
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13.
Blaise?TF?Alako Antoine?Veldhoven Sjozef?van Baal Rob?Jelier Stefan?Verhoeven Ton?Rullmann Jan?Polman Guido?JensterEmail author 《BMC bioinformatics》2005,6(1):51
Background
High throughput microarray analyses result in many differentially expressed genes that are potentially responsible for the biological process of interest. In order to identify biological similarities between genes, publications from MEDLINE were identified in which pairs of gene names and combinations of gene name with specific keywords were co-mentioned. 相似文献14.
The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster 总被引:3,自引:1,他引:3
Schug MD; Hutter CM; Wetterstrand KA; Gaudette MS; Mackay TF; Aquadro CF 《Molecular biology and evolution》1998,15(12):1751-1760
In a recent study, we reported that the combined average mutation rate of
10 di-, 6 tri-, and 8 tetranucleotide repeats in Drosophila melanogaster
was 6.3 x 10(-6) mutations per locus per generation, a rate substantially
below that of microsatellite repeat units in mammals studied to date (range
= 10(-2)-10(-5) per locus per generation). To obtain a more precise
estimate of mutation rate for dinucleotide repeat motifs alone, we assayed
39 new dinucleotide repeat microsatellite loci in the mutation accumulation
lines from our earlier study. Our estimate of mutation rate for a total of
49 dinucleotide repeats is 9.3 x 10(-6) per locus per generation, only
slightly higher than the estimate from our earlier study. We also estimated
the relative difference in microsatellite mutation rate among di-, tri-,
and tetranucleotide repeats in the genome of D. melanogaster using a method
based on population variation, and we found that tri- and tetranucleotide
repeats mutate at rates 6.4 and 8.4 times slower than that of dinucleotide
repeats, respectively. The slower mutation rates of tri- and
tetranucleotide repeats appear to be associated with a relatively short
repeat unit length of these repeat motifs in the genome of D. melanogaster.
A positive correlation between repeat unit length and allelic variation
suggests that mutation rate increases as the repeat unit lengths of
microsatellites increase.
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