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The first two concepts were incorporated as two independent scores, measuring the conservation of the protein among Gram-negative organisms and among different strains of the same species, respectively.
Ultimately, we are interested in measuring the conservation of microsatellites of any length, and therefore detailed models of microsatellite expansion and contraction may be unnecessarily complex for our purposes.
The final formula to compute the co-evolution score C between two genes X and Y is then: (9) C (X, Y ) = ϕ (X, Y ) * D (A, B ) 3 * K (X, Y ) with ϕ X,Y) the correlation score between phylogenetic profiles of the genes X and Y, D A,B) the distance between the most distant organisms A and B in which the genes X and Y co-occur and K X,Y) a factor measuring the conservation of genes neighborhood.
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It provides a globally accepted standard with which to measure the conservation status of species over time.
Accordingly, the aim of this study was to measure the conservation success of a PA, comparing its land use and cover change over time in different management categories.
To measure the conservation of CGs in other species, the mRNA and EST libraries of 23 other vertebrate genomes were downloaded from the UCSC Genome Browser database.
3. Group-3 (g3) measures the conservation elements in the assemblies.
RDD [ 5] values were calculated to measure the conservation of distance between the HCEs pairs.
Thus, for these regions, the CHAOS sequences are in fact better than the UCSC sequence to measure the conservation.
Herein, the Position Specific Iterative BLAST (PSI BLAST) was employed to measure the conservation status for a specific residue.
To measure the conservation of proteins, we find orthologous proteins in other species, instead of sequence alignment using BLAST.
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