WebMeanwile, Ka/Ks of CalS homologous pairs were calculated to further understand the adaptation of the CDS region of CalSs (Fig. 4, Table S5). Most of the homologous gene pairs Ka/Ks < 1, and about 94.6% gene pairs had a Ka/Ks ratio less than 0.5, which meant that almost all gene pairs underwent purification selection. WebOnline tools The ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitution rates is an indicator of selective pressures on genes, and can be used to …
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WebJul 2, 2024 · This similarity data was then used to create a tab-delimited text file required to calculate Ka/Ks in TBtools software. In addition to evolutionary relation, the phylogeny of the PvDDPs was also investigated within the study. The multiple sequence alignment of common bean DUF221 domain-containing proteins was firstly performed using Muscle. WebHere, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit … lowest used rv loan rates
Genome-wide identification and expression analysis of the
WebFeb 14, 2024 · Moreover, the Ka/Ks ratios were calculated by TBtools . 4.7. Expression Pattern of CebHLHs. Total RNA from four different color sepals was extracted using the OMEGA kit (Norcross, Georgia, USA). RNA-seq and library construction were performed by the Novogene Bioinformatics Co., Ltd. (Beijing, China) on an Illumina HiSeq 2500 … WebJan 15, 2015 · This ratio has been used in several ways: 1) to enhance gene predictions as areas of coding sequence will have a lower Ka/Ks ratio than non-coding areas; 2) determine differences in natural selection pressure on proteins. Neutral selection (Ka/Ks = 1) occurs when coding sequences ; Positive selection (Ka/Ks > 1) Purifying selection (Ka/Ks < 1) We used the STRING database to predict potential interactions among the PeHsf proteins (Fig. 12 and Supplementary Table S6). There were 19 nodes in the PeHsf protein interaction network, each of which interacted with multiple other nodes. Some proteins exhibited direct interactions, e.g. PeHsf14 and PeHsf16, … See more Forty-four putative HSF candidate genes were obtained from an HMMER3 search of the bamboo protein database using the plant HSF-type DBD model (Pfam … See more To clarify the evolutionary relationships among the HSF proteins, amino acid sequences of 41 moso bamboo HSFs, 25 rice HSFs, and 21 Arabidopsis HSFs were … See more The number of introns in each moso bamboo HSF gene ranged from one to three (Fig. 3). Approximately 75% of the genes contained a single intron, whereas six … See more The PeHsf genes were non-uniformly distributed across the 19 chromosome scaffolds of moso bamboo (Fig. 6). The largest number were found on scaffold 21 … See more january public holidays nz