Sentence examples for matrix for nucleotide from inspiring English sources

A scoring matrix for nucleotide words of length l is an { A, C, G, U} × l matrix M = (m bk ).

All the alignments were done using WU-BLAST v2.0 [ 50], with identity matrix for nucleotide alignments and BLOSUM62 identity matrix for protein alignments.

Multiple sequence alignments were generated with MAFFT v7.017, using the FFT-NS-ix2 algorithm and the BLOSUM62 scoring matrix for protein alignment and the automatic algorithm and the 200PAM/k=2 scoring matrix for nucleotide alignment (Geneious Pro software).

Tree construction was achieved by the neighbor-joining method with the complete deletion option using the Jukes-Cantor matrix for nucleotide sequences and the PAM (Dayhoff) matrix for protein sequences, respectively.

Cyt b was aligned by eye while RAG sequences were aligned using the online version of MAFFT 6.822 [ 46] using the accurate G-INS-i algorithm with the scoring matrix for nucleotide sequences set to 1PAM/K=2, a gap opening penalty of 1.53 and an offset value of 0.1.

Distance matrix for nucleotides was calculated according to the Kimura's two-parameter model [ 24].

We use the BLAST substitution matrix for nucleotides [ 15] for local N-maps and Identity matrix for global ones.

The frequency matrix for nucleotides at each position (Table 4) was constructed using sequences found in known Ste11 target genes [ 14].

Evolutionary analyses and phylogenetic tree were constructed using the software Mega 6.0 [ 31] with the neighbor-joining method [ 32] from a distance matrix corrected for nucleotide substitutions by the Kimura two-parameter model [ 33].

A bootstrap phylogenetic tree demonstrating the relationship between the isolates was created using the maximum-likelihood method [ 41] and a distance matrix corrected for nucleotide substitutions based on the Kimura 2-parameter model [ 42].

In addition, a compatibility matrix of nucleotide substitutions was constructed using the software S ites[ 71] to search for possible recombination blocks in the datasets.