Hence, the more base pairs (x i, x j ) there exist in the set of structural alignments, the more gain in the gain function is given for the prediction y ij = 1.
Mulder et al. [ 35] mapped GO terms to the domain if all proteins with the given domain do not exist in the set of proteins without the given GO term.
The negative set meets the two requirements: (i) the noneffective pairs cannot exist in the set of 76 effective pairs, and (ii) the number of noneffective (negative) pairs is equal to that of effective (positive) pairs.
For this purpose, we compiled a set of (position, amino acid) pairs containing all pairs that existed in the set of correctly classified sequences and were different from the (position, amino acid) information of the consensus sequence.
The well-known diversity of lifestyles of disparate apicomplexans as well as the age of the phylum (700-900 million years [ 16]) led us to hypothesize that significant differences exist in the sets of transcription factors present in each species.
These 14 cases were selected here to exemplify the domain of science and medicine, but the same diversity exists in the larger set of 102 cases.
It can be seen that only a little difference exists in the two sets of result.
Having been done in different ways and with different organisms, not surprisingly, little overlap exists in the different sets of protective genes that have been reported.
For example if the basis set "LANL2DZ" is used in a QM calculation, but no corresponding entry exists in the basis set dictionary, the name of the basis set will still be stored in the database when publishing the data to allow queries on the calculation.
The list of differentially-regulated genes in the current data set for which orthologs exist in the data set of Martinez et al. [23] are listed in Table S3 and a schematic representation of numbers of differentially-expressed genes identified by Martinez et al. [23] that were also upregulated in endometrium and blood is in Figure 3.
