Gene Morphing System

[…] the snp calling analyses were performed based on these reads., we obtained three sets of snp calling results generated by the genome analysis toolkit (gatk), samtools and genotype model selection (gems), respectively. we implemented strict criteria to filter potential false positive snps (please refer to the materials and methods for details). on average, the gatk obtained 823.34 snps, […]

[…] software applications have been created to aid gene redesign and customization for synthesis. few of these tools were unattainable at the time of this study. these include upgene (gao et al., ), gene morphing system (gems) (jayaraj et al., ), and gene composer (lorimer et al., ). the basic functionality of these programs can be largely found in other currently available tools., […]

[…] gc content, minimization of hairpin structures within the gene, and/or of secondary structures in the n-terminal codons [, ]. the free software tools proposed in literature include, for instance, gems (web-based application, []), optimizer (web-based application, []), synthetic gene designer (web-based application, []), and gene designer (stand-alone application, []). all the tools mainly […]

[…] series of new methods such as the dual asymmetric pcr and assemble pcr were developed , . to facilitate the design and assemble of the oligonucleotides, softwares such as dnaworks , gene2oligo , and gems were developed to make all the oligonucleotides thermodynamically unity. however, such one-step gene synthesis method has its limitations in synthesizing long dna sequences., generally, […]

[…] recommended protocol. all other reagents were obtained from sigma (usa), seven versions of the calf prochymosin a gene were designed and constructed. the variant v0 was designed using the software gems [] and a codon table containing only the most abundant codon found in the entire genome of e. coli w3110 for each amino acid. the variant v1 was designed using the one amino acid-one codon […]