Sentence examples for based on coding sequences from inspiring English sources

Polymerase chain reaction primer pairs for mRNA quantification, intending to flank at least one intron, were designed based on coding sequences obtained from the GenBank Sequence Database (http://www.ncbi.nlm.nih.gov/Genbank/index.html) (Table 1>).

Conventionally, orthologs are established by one-to-one or many-to-many relationships through phylogenetic reconstructions based on coding sequences and conservation of protein domains [ 21].

Specific primers for TRPM8 channel were designed based on coding sequences.

For phylogenetic reconstruction based on coding sequences, we estimated the best-fit model of sequence evolution to be HKY + I + G (base frequencies  = 0.2130, 0.3327, 0.4543; proportion of invariable sites  = 0.4169; gamma distribution shape parameter  = 0.8145) based on the AIC in Modeltest 3.7 [58].

To obtain initial sequence information for the isolation of the wt1 gene, degenerate primers (Table 1 – wereF1a; WT1 R1a; WT1 F1b; WT1 R1b; WT1 F5) were designed based on coding sequences of this gene from D. rerio (NM_131046; NM_001039634), A. japonica (AB030741) and O. mykiss (AF334670; AF334670).

To this end, we contrasted phylogenies based and coding and noncoding sequences, and compared rates of synonymous and nonsynonymous substitution along the tree based on coding sequences.

This analysis also revealed that some genes thought to be single-copy have paralogs (based on coding sequence) in some species, of which 8 paralogs in 7 genes had a sufficiently conserved TSS to be included in the analysis (Table S1).

For all methods based on coding sequence similarity, the longest proteins were used as the representative proteins of the genes.

We also conducted separate phylogenetic reconstructions based on coding sequence, intron 2 sequence, and the 5′ and 3′-flanking sequences of each gene.

This suggests that in these cases local synteny based orthology assignments are more often concordant with gene structure evidence (ICR) than those based on coding sequence similarity.

Therefore, a revised 520 amino acid protein based on coding sequence from 8 exons is described in this study (see Additional File 1: revised sequence for LOC241768).