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We used BioEdit to introduce IUPAC degenerate codes (i.e. those representing different sets of nucleotides) across sequencing electropherograms.
Though L. bicolor exons can be short, isolated alignments of small sets of nucleotides bracketed by spaces in the BES should be discouraged.
These tests may identify different sets of nucleotides potentially under selection.
To better understand the role of negative selection, we compared the multispecies conservation of sets of nucleotides with that of the same nucleotides within nearly neutrally evolving regions.
However, as we documented in Shah and Gilchrist (2011), Δ M for similar sets of nucleotides differs significantly between amino acids.
For other datasets with greater genomic biodiversity (heavier taxonomic sampling), it may be feasible to evaluate much smaller sets of nucleotides; the tradeoff is in the high variance of parameter estimates with the smaller data sets.
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Microarrays like Affymetrix GeneChips measure mRNA expression of genes using sets of nucleotide probes.
In an earlier paper, we described a method for creating "indicator vectors" representative of sets of nucleotide sequences [6].
Compared to other databases (e.g., TRANSFAC, JASPARR motifs are non-redundant and are derived exclusively from sets of nucleotide sequences experimentally demonstrated to bind TFs.
In the forward primer region of the 10 individuals, there were two sets of nucleotide sequences that differed by less than 7 bp.
Comparison of different sets of nucleotide sequences was analysed by the Best-Fit sequence alignment program (Needleman and Wunsch, 1970; Smith and Waterman, 1981).
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