Attempts to optimise specificity by further editing the Cep290 protein alignment failed to produce significant improvements in homologue identification.
Detailed analysis of the sequence alignment failed to identify any compact region in the primary sequence that would be specific for one or the other isoform across the analysed plant families.
However, the aligner fails to find the proper alignment because it does not consider all possible alignments crossing splice junctions owing to the search complexity.
Additionally, approximately 5%% of RNA alignments failed to map to a gene with an assigned symbol, likely corresponding to unannotated structural or regulatory RNAs.
Although basic sequence alignments fail to reveal orthologs in other organisms, K10D2.4 has been proposed to be orthologous to the human C10orf104/APC16 gene (Kops et al. 2010).
Also in comparison to the best structural models (TM-align and PPM models) the difference is very large, which indicates that sequence-based alignments fail to produce any reasonable model for many cases (at least at the fold level).
The more sensitive multiple alignments failed to record any human-rodent syntenic regions involving the SULT1A1, SULT1A2, or SULT1A4 loci but detected synteny involving the SULT1A3 loci and both rodent genomes.
The decrease in the sensitivities of all methods can be explained by the fact that the alignment tool fails to align increasingly noisy RF reads.
EnsemblPlants provides highly interactive web interfaces to show phylogenetic tree and alignment summary graphically, but fails to show alignment in details.
