One interesting alternative to LD-based haploblocks are genomic prediction methods based on identity-by-descent (IBD) relationships [ 5, 6]; this alternative benefits from linkage analysis over the genomic data.
TABLUP and GBLUP have some features that other genomic selection methods based on model (1) lack.
Animal model genomic prediction methods based on genotype imputation on a national scale were developed, and the most accurate method, GLDLA0BLUP, combined linkage and linkage analysis information.
In other species, for which dam families are more important (e.g. pigs and poultry), the sire model will not fit so well, and the advantage of the genomic selection methods based on an animal model will increase compared to the dairy cattle situation.
Two types of methods have been used to detect HGT events in genomic sequences: Phylogenetic methods, based on the examination of the phylogenies of individual genes or proteins; and compositional methods, based on the analysis of DNA composition, which is assumed to contain some evolutionary information in the form of species-specific signatures.
However, even these methods generate false positives, and, we used additional methods based on genomic information to add confidence to our assignment of sequences to the helical cytokine family.
In recent years, many bioinformatics methods have been adapted to PPI calculations and have been categorized into four types of methods: methods based on genomic information; methods based on evolutionary relationships; methods based on protein sequences (ab initio); and methods based on protein 3-dimensional structural information.
Methods based on genomic approaches and amongst them global gene expression profiles play an increasing role in such efforts.
Methods based on genomic comparison, detection of composition bias and search of mobility genes are the most performing tools for the flexible genome characterization [ 45].
This approach of analysing metabolism as a single network allows a global view of functional processes, which was enabled by metabolic reconstruction methods based on genomic data [ 33- 37].
