This approach risks to be hampered by sequence conservation due to functional homology in different organisms.
The 5' ends of these sequences, whether defined experimentally (LSUE and LSUG from C. cohnii) or by sequence conservation, are also very similar to those of their Plasmodium counterparts.
We propose that conservation of secondary structure of the well-conserved domains (defined by sequence conservation and the presence of highly conserved amino acids) probably reflects conservation of catalytic functions and/or protein-protein interactions of these domains.
To compare methylomes of human and mouse PGCs, we lifted over published mPGCs BS-seq data (Kobayashi et al., 2013) to the human genome by sequence conservation and compared CpG methylation at conserved repeat-free 1 kb tiles.
In this section, we will report the experiments conducted to evaluate the performance of our proposed approach, ProteRNA with the combination of SVM-based classifier with evolutionary profiles and conserved residues discovery by sequence conservation.
In this article, we proposed the prediction framework "ProteRNA" with the combination of SVM-based classifier with evolutionary profiles and conserved residues discovery by sequence conservation for identifying RNA-interacting residues in a RNA-binding protein.
The Type I RM systems encoded by the bacterial species used as the sources of the ArdA proteins examined here, namely, E. faecalis, B. fragilis and S. aureus, do not belong to the same family when assessed by sequence conservation (data not shown, sequences of Type I RM systems obtained from REBASE [25]).
The alignments with homologous sequences at the protein level enabled us to localize conserved coding regions and to determine the frame of the coding sequences within boundaries defined by sequence conservation.
In this study we show that the parasitic protist, E. histolytica, thought to be an early branching eukaryote, possesses the major classes of snoRNAs as judged by sequence conservation with yeast and human.
(b) Corresponding molecular surface for a coloured by sequence conservation as in Fig. 1b.
