Analysis of P. pacificus genomic sequence also identified candidate NHR-67 and NHR-239 orthologs by conservation of DBD sequences, but failed to identify coding sequences or gene assembly models with similarity to TLX/TLL and NHR-239/Hr83 clade LBDs (data not shown).
Lichtarge et al. [ 26] proposed a method called evolutionary trace to predict functional sites by analyzing the conservation of sequence subgroups.
The EvoPrinter algorithm [ 5] creates an array of nucleotide strings from each of the selected alignments and then looks for conservation of sequence by looping through each of the strings one base at a time, outputting an uppercase base for only those input reference DNA nucleotides that are aligned in all of the different c eBLATs included in the analysis.
Serologic cross-reactivity of Anaplasma spp. is caused by conservation of major surface protein sequences (7 ). A. phagocytophilum infection usually resolves after treatment with doxycyline for 4 days (8 ).
The final assignment of identity was guided by conservation of topology, synteny, and overall sequence such as the conservation of functional domains, including intracellular sequences that mediate interactions with the key signal transduction pathway used by cytokine receptors, the Jak-Stat (Signal transducer and activator of transcription) pathway [ 53].
It is thought that this high-level sequence variability, accompanied by conservation of many yeast-type physiological and morphological traits, is due to stochastic genetic drift, characteristic of the evolution of unicellular Saccharomycotina species [ 85, 92].
From the last few years, computational approaches have been widely used to detect the impact of deleterious nsSNPs in candidate genes by analyzing data such as conservation of sequences across species [ 22], physicochemical properties of the polypeptides [ 23, 24], and structural attributes [ 25].
In rice, many annotated miRNAs have been identified by computational predictions, based on the conservation of sequences with Arabidopsis miRNAs [31].
Such annotation is generally based on known functions of similar gene sequences in other organisms, a type of analysis made possible by evolutionary conservation of gene sequence and function across organisms as a result of their common ancestry.
A large number of human and mouse candidate cis-regulatory modules, predicted by interspecies conservation of noncoding sequences [ 5], EP300 occupancy [ 7], or other features [ 51], have been tested for the ability to increase expression of a beta-galactosidase reporter gene driven by a minimal promoter in a tissue-specific manner at embryonic day 11.5 of mice.
