Typically, we refer to the fused gene as a 'composite' protein, while the un-fused counterpart genes in the reference organism are referred to as 'component' proteins [ 1, 3].
Many laboratories have adopted Chlamydomonas reinhardtii as a reference organism for discovery of algal-specific adaptations of TAG metabolism.
For this purpose, we used "Camelus dromedarius" as the reference organism in the RepeatMasker algorithm.
On one hand our method is a good way to eliminate processes and organisms for which the reference organism is not a good model.
To protect against infection, D. melanogaster employs a suite of cellular and humoral defense mechanisms, making it a good reference organism in which to dissect host responses (reviewed in [1], [2], [3], [4], [5], [6]).
Both methods had a modest number of reads that failed taxonomic assignment because the read's sequence identity to the reference organism was below the stringent identity threshold (316 Enz+Sanger reads, between 791 and 2932 Enz+pyrosequencing reads).
Because it has coevolved the majority of its DNA replication, repair, and recombination mechanisms with K. radiotolerans we chose it as a reference organism, together with E. coli and.
Sites can also be classified by non-evolutionary relationships such as the number or identity of organisms involved (e.g. only homologous sites involving an important reference organism such as Homo sapiens), or even by ordering relationships relative to other homologous nucleotides (e.g. collinearity).
Multiple species of bacteria and hundreds of strains thereof are being sequenced every year, thanks to cutting edge approaches such as re-sequencing wherein genome sequence of a reference organism is used as a scaffold to direct analysis of several different strains [1].
Homo Sapiens has been used as reference organism.
This implies that at least 80% of the reference organism subsequence had to match the alignment.
