2079 additional 3' cDNA ends, with two or more identical sequences obtained independently, were detected within the coding region of 854 genes without obvious σ70 or σ38 promoter elements.
The search returned either a single match (i.e., where the query sequence was returned as the most likely match) or as multiple matches (i.e., where the query sequence plus one or more identical sequences were returned as equally likely).
B. Within the cluster of outbreaks, there were two or more identical sequences from different outbreaks.
Additionally, we only included variants with two or more identical sequences in the analyses, which should ensure exclusion of random sequence errors.
The amino acid data showed more identical sequences owing to synonymous substitution, as can be seen when the nucleotide and amino acid patterns of patient RF15 are compared.
Therefore, we identified sets containing two or more identical sequences and removed (at random) all but one copy of each identical sequence; this further reduced our data set to 16,639 gene sets (N ≥ 4) with 119,695 genes (open reading frames).
ClustalW [ 52] alignment was used to eliminate redundancy, by setting the following two criteria: (i) where a cluster contained two or more identical sequences, the longest was retained, and (ii) where the members of a cluster fell into recognisable sub-groups, only one member of each sub-group was retained.
If there were two or more identical protein sequences in a locus, we selected one sequence with the longest transcript.
(76) Because the four domains of the NaVs 76) are more identical in sequence to the corresponding domains of CaVs than to each other and have in turn the lowest levels of identity with KVs, it was suggested that a single gene gave rise to (first) potassium and (then) calcium channels.
The presence of single-domain sodium channels from primitive prokaryotic organisms that are more identical in sequence to eukaryotic NaVs than to other members of the voltage-gated ion channel family indicates they may have diverged from KVs at an earlier stage, before gene duplication (in eukaryotes) had taken place.
