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Sentences for "cogs "
It's as though after wrestling long and hard with Cézanne's dictum that the artist should paint the world of nature in terms of spheres, cylinders, and cones, Léger realized: Hey, here's an environment that's actually made of these shapes! The cogs and pistons that dominate his paintings of the early 1920s remain unusually intimate, human-scale.
Anyway, Me is kind of a comic book, very heavy on graphics like you used to find in Johnson and Smith catalogs, and rife with bold print emphasizing nothing in particular: Fairbanks White Blaze Vanderbilt Used Rambler Alcan Highway The post office The cogs simply do not mesh As a bear would say goodbye to a leg trap That's not bad.
The cogs in her brain turn feverishly.
It would be desirable to automate this procedure, but the best automated methods for subfamily annotation, such as the COGs database [ 10 ] , are clustering methods that do not directly use phylogenetic analysis.
Presence-absence of genomes in COGs The topology of the parsimony tree built using this criterion appears to reflect primarily the phenotypes of the respective organisms (Fig.
Briefly, the COGs were constructed from the results of all-against-all BLAST [ 37 ] comparison of proteins encoded in complete genomes by detecting consistent groups of genome-specific best hits (BeTs).
A pair of genes from two COGs was considered to be conserved if the respective genes were adjacent in at least one genome and were separated by no more than two genes in at least two additional genomes.
Parsimony trees based on the representation of genomes in orthologous gene sets The information on orthologous genes in prokaryotic genomes and the yeast genome was derived from the COGs as in the previous approach, and the orthology data were similarly represented as a 0/1 matrix of presence-absence of the analyzed genomes in the COGs.
QuartOPs are similar to the clusters of orthologous groups (COGs) maintained by the NCBI [ 26 27 28 ] , but differ in that COGs require only unidirectional, circular best hit relationships for three of the reference genomes, whereas we require the reciprocal top hit relationship for the four genomes included in a quartet, and we do not limit our identification of QuartOPs to a number of reference genomes.
The method for identifying probable orthologs is based on the genome-specific best hits (BeTs) rationale that underlies the construction of the COGs database [ 4, 5].
Only COGs with one representative (ortholog) from each genome (COGs of size 3) were considered for further analysis.
The BeT procedure was used to identify perfectly symmetrical COGs of size 3 for this species group.
Because these mammalian genomes are not complete, a formal possibility exists that the COGs procedure will isolate non-orthologous protein sets.
Subsequent to the construction of human-mouse-rat COGs and phylogenetic trees, the 'triplet test' [ 17] was used to further ensure that the COGs of size 3 contained only orthologs.
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