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The most obvious sequence signature to start this bioinformatic search was the one found in Tff subunits: the distinctive class III signal peptide motif (Fig. 3) (Dalrymple and Mattick, 1987; Szabó et al., 2007).
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Sequencing data are the most obvious example as 'deep sequencing' platforms become universally adopted.
The most obvious source of a sequence that might be able to activate expression of the rightward genes in our new piggyBac vectors was the downstream 3'-TRD, which includes the piggyBac 3' terminal repeat and a 172 bp internal domain sequence with an 83% AT content [ 4, 18].
In the case of Ectocarpus, because screening isolated the one copy of the viral sequences, the most obvious explanation is that these viral sequences are remnants of one ancient viral infection.
Such frameshifts and stop codons are the most obvious indicators of coding-sequence decay.
The most obvious, is that the sequences in question are related to known Apis proteins, but they mainly contain untranslated regions (UTRs) and therefore do not produce significant "hits" in BLASTX alignments.
Although inference of orthology is most obvious via overall comparisons of sequence similarity, it is conceivable that other sources of information may be useful.
We already discussed the most obvious problem with using genomic (sequence) data and associated predicted binding sites, namely the large number of mis-predictions.
This difference was most obvious when the full polyprotein sequences were compared (Figure 6).
The first and most obvious difficulty is that nucleotide sequences must have enough variability within and among the studied species to obtain an adequate resolution of the phylogenetic tree.
The principal differences between the original HFA and the repeated SRSF screen relate to the libraries used, and whilst the most obvious difference is to the sequences of the dsRNAs that make up the library itself, other factors may also be significant.
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