Sentence examples for default nucleotide from inspiring English sources

The default "Nucleotide BLAST" for the "BLAST at NCBI" search criteria were used.

The default nucleotide substitution model (HKY85) was selected assuming an estimated proportion of invariant sites and 4 gamma-distributed rate categories to account for rate heterogeneity across sites.

For estimation of quality using assembled reads to the 103 kb exemplar sequence [ 16] BLAT [ 17] was used with a 95% identity cutoff (otherwise with default nucleotide options) to identify strongly matching reads.

For the PB2, PB1, PA and NP segments, the SRD06 nucleotide substitution model [ 56] was chosen as the default nucleotide substitution model (preferred over GTR model with log BF from 3242 to 3289), which allows one Hasegawa, Kishino and Yano (HKY) model [ 57] for codon positions 1 and 2 and a different HKY model for position 3, together with gamma-distributed rates across sites.

By default, only nucleotide sequences are presented, but the protein view is accessible using a simple switch at the top of the page.

By default each nucleotide is represented in the network by three nodes, positioned at the P atom of the phosphate group, C4′ in the base and C2 in the sugar ring.

BLAST searches were performed using default parameters for nucleotide sequences against the human nucleotide database [ 33] and the miRNA registry [ 60].

In ML analyses, the JTT substitution model for amino acids or the HKY (default) model for nucleotide substitutions was used.

The well-aligned regions were selected (1,122 sites in total) with Gblocks under the default condition for nucleotide sequences.

Thirdly, the poorly aligned regions were removed from each alignment using Gblocks version 0.91 b (Castresana 2000) with default parameters for nucleotide sequences.

Conservation Index values were calculated using the Rate4Site application, a stand-alone program within the ConSurf server, using default settings for nucleotide sequences.