Sentence examples for based on nucleotide identity from inspiring English sources
A total of 187 metagenomic clones identified as being Syn OS-A or Syn OS-B'-like (based on nucleotide identity of either the sequence or its clone-mate to the genomes) were found to contain Type I (43 clones), Type II (139 clones) or Type III (5 clones) CRISPRs.
The latter was implemented in DnaSP v5 [ 33] to identify haplotypes that were shared amongst isolates based on nucleotide identity.
A distance matrix was then calculated using MEGA5, and the genes were grouped based on nucleotide identity (>90%).
There are 36 opossum TRBV segments and these can be grouped in 28 subgroups based on nucleotide identity with the value between subgroups ranging from 38.5 to 68.5%.
There are nine TRGV gene segments present in the opossum and these are divided into four subgroups based on nucleotide identity.
All PCR products were clones and sequenced as described in Additional file 2. Partial and full-length CYP4 nucleotide sequences were clustered by Sequencher 4.6 based on nucleotide identity (> 80% identity), aligned using ClustalX [ 32] and this alignment was used to construct maximum parsimony trees using PAUP*4.0b10 [ 33].
In order to investigate more closely the relatedness of CT genes in these two species, we sought putative human and chimpanzee orthologues for as many CT genes as possible, based on nucleotide sequence identity to the cognate human transcript sequence.
To create a distribution of percent identity based on nucleotide composition, 10,000 permutations were completed for each sequence and P-values were obtained using the empirical cumulative distribution function for each set of permuted alignments (in R).
To our knowledge, there is no clear definition of a nebovirus genotype based on nucleotide or amino acid sequence identities.
The position of each OTU and the accession number of reference sequences are shown in the phylogenetic tree (Fig. 4), while the closest relative(s) based on nucleotide sequence and deduced amino acid sequence identity are assigned in Additional file 1: Table S2.
Here we classified previously-identified TRDV1 cloned cDNA sequences based on several criteria which included their relative placement in trees based on nucleotide and deduced amino acid sequences, specific sequence characteristics and percent identities based on nucleotide sequence alignments (data not shown).
