The structural organization of the archaeal RNA polymerase serves as a reference for future structure function analysis of the transcription mechanism and allows for evolutionary comparisons.
Selecting suitable species is the key for evolutionary comparisons.
Thus, ITS2 has been considered a double-edged tool for evolutionary comparisons in eukaryotes [ 12].
The plant specific database used for evolutionary comparisons was obtained from.
As genomic resources for V. destructor continue to improve, opportunities for evolutionary comparisons with other arthropods will be enriched.
Marsupials diverged from eutherian mammals about 148 million years ago (MYA), and mammalian Subclass Theria that contains these groups diverged from monotremes (Subclass Prototheria) about 166 MYA [ 20], so comparisons between these major mammal groups provide depth for evolutionary comparisons.
Moreover there is complete genome sequence of several other yeast species for evolutionary comparisons, and extensive protein interaction data between protein pairs are available in the Database of Interacting Proteins (DIP) [ 14].
For example, protein-interaction networks have been used for evolutionary comparisons among organisms (Wuchty et al., 2003), for identifying functional modules and network motifs (Spirin and Mirny 2003) and for predicting functional annotations based on network connectivity (Schwikowski et al., 2000).
For evolutionary comparisons, we compiled RNA-seq data containing mouse snRNAs from several types of cells and tissues (Table 1), including embryonic stem (ES) cells, differentiated ES cells, fetal head, cerebrum, and testis (Cui et al. 2010; Yang et al. 2011).
For example, evolutionary comparison of GPCR sequences between species can help to identify conserved motifs and may recognize key functional residues [ 11- 13].
