Because there was sequence variation for each gene from amplicon sequencing, more than one sequence per gene was used for reference (Additional file 3, 4, 7 and 8).
Applying RECIST criteria in the MRI-based assessment of irradiated liver metastases is challenging, because there are multiple sequences obtained with MRI. 9 We assessed response based on consistent imaging sequences (T2) across the studies.
Directed evolution studies also suggest that epistatic paths can be bypassed (and they certainly are in laboratory evolution), because there are multiple sequences that satisfy a given fitness goal, and there are many different paths to these sequences [34], [71], [72].
Because there are no sequence data available from heterotrophic Paulinella species with a taxonomic identification, we could not provisionally identify the source of the environmental samples.
Because there are no sequence changes that are unique to clade IB versus IA and II, the variable response to interferon-γ is likely to be an effect of more than one sequence change.
Because there are no sequence information about Anticarsia gemmatalis, except for a fragment of actin gene (amplified by PCR using universal primers designed ad hoc in our laboratory) [ 15], that sequence was used as an internal standard in mRNA assays.
In C. elegans, the flanking nucleosomes are positioned closer together than in yeast, presumably because there are no sequence-specific DNA-binding proteins between the centromeric and the flanking nucleosomes.
Transmissible mink encephalopathy (TME) agent was used as a control because there are multiple sequence differences between mink and BHS prion proteins and because a previous study indicated limited transmissibility of TME to domestic sheep (Cheviot breed) with an extended incubation period (mean: 65 mo) and with only about 25% penetrance [ 29].
In the wheat genome, gene annotation using full-length cDNA sequence data is essential, because there are many repetitive sequences and retrotransposons that can cause confusion when trying to predict the gene regions in genomic sequences [see examples in reference [ 9]].
ATP6 sequences were analysed with Basidiomycota sequences from our lab (unpublished data by SG) because there are no available sequences in GenBank for Sebacinales.
