Sentence examples for based on coding sequence from inspiring English sources
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.
However, local synteny has a slightly higher FN rate than the four orthology methods based on coding sequence similarity (BLASTP, SBH, RBH and Inparanoid).
We also conducted separate phylogenetic reconstructions based on coding sequence, intron 2 sequence, and the 5′ and 3′-flanking sequences of each gene.
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).
These transcripts were clustered into genes based on coding sequence (CDS) evidence using a revised protocol which we previously proposed [ 21].
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].
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).
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].
