Synthetic biology software tools and databases

Synthetic biology aims to create functional devices, systems and organisms with novel and useful functions on the basis of catalogued and standardized biological building blocks. Although they were initially constructed to elucidate the dynamics of simple processes, designed…

Synthetic biology steps

Bioinformatics tools

Databases

Most recent bioinformatics tools

CAIcal
Web
Desktop

CAIcal Codon Adaptation Index cal

Calculates the Codon Adaptation Index (CAI) for a group of sequences using…

Calculates the Codon Adaptation Index (CAI) for a group of sequences using different reference sets. CAIcal is a web-server that includes a complete set of tools related with codon usage adaptation…

PromCal
Desktop

PromCal

Allows evaluation of experimental data. PromCal is a web tool developed to…

Allows evaluation of experimental data. PromCal is a web tool developed to provide a tool for calculation of relative promoter strengths from experimental data. The software can be applicable in…

RCDI/eRCDI
Web
Desktop

RCDI/eRCDI Relative Codon Deoptimization Index / Expected RDCI

Performs calculation of the Relative Codon Deoptimization Index (RCDI) and a…

Performs calculation of the Relative Codon Deoptimization Index (RCDI) and a new expected value for the RCDI (eRCDI). RCDI/eRCDI is a program available both as one of and the tools of the CAIcal…

CUT
Web

CUT Codon UTilization tool

Allows analysis of all genes or transcripts banked for a species. CUT is based…

Allows analysis of all genes or transcripts banked for a species. CUT is based on a standard “Model View Controller” (MVC). It methodically counts the codon content in gene or transcript…

Most popular analytical software and databases

Addgene
Dataset

Addgene

Archives plasmids generated by scientists, conducts quality control, annotates…

Archives plasmids generated by scientists, conducts quality control, annotates the associated data and makes the plasmids and their data available to the scientific community. Addgene is a non-profit…

Curators for Synthetic biology

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