Conducts next generation sequencing (NGS) investigation. Geneious provides visual sequence alignment and editing, sequence assembly, comprehensive molecular cloning and phylogenetic analysis. It increases process efficiency and improves data organization. This tool enables the importation and conversion of a vast range of data types and offers a solution to customize researchers’ algorithms.
A web application for designing synthetic promoters with altered transcriptional regulation. PromoterCAD is built on the LinkData open platform for data publication and rapid web application development, allowing new data to be easily added, and the source code modified to add new functionality.
A web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes.
Measures long-range correlations in DNA sequences. CorGen is a web application that generate random sequences with the same (or user-specified) correlation and composition parameters. It offers three different types of services: (i) measuring long-range correlations of a given DNA sequence, (ii) generating long-range correlated random sequences with the same statistical parameters as the query sequence and (iii) generating sequences with specific userdefined long-range correlations.
Calculates covariance scores for constrained regions of background conservation. McBASC can be utilized as a covarying or highly conserved filter. This software gives an equally high score to conserved or covarying alignments and allows, without a reduction in score, substitution of conserved pairs of residues for covarying ones.
Automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries.
A web-based tool that translates a textual description of a synthetic biology design into an image. Pigeon allows programmatic generation of design visualizations, is easy to learn, is easily extensible to new glyphs and notation, and can be connected to other software tools for visualizing their output.
Aims to assemble multiple DNA fragments in a single reaction using a standardized assembly design. MIDAS is a program useful for constructing genes from libraries of sequence-verified and contains features allowing genes to be nested between other genes or genetic elements. It permits researchers to create libraries of cloned genetic parts, as libraries of promoters, coding sequences (CDSs) of genes of interest, transcriptional terminators, or fusion tags.
Automates synthetic DNA design process. BOOST can determine a sequence that can be synthesized via a trial-and-error process. This software provides DNA synthesis design functionalities that can operate on batches of annotated sequences. It utilizes a different method to check each type of gene synthesis constraint and formats the resulting violation report by constraint type to verify DNA sequence against common DNA synthesis constraints.
Provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions.
Permits multi-level partitioning of large-scale DNA constructs for synthetic biology applications. Genome Partitioner is a web-tool that provides a detailed online documentation including explanation of partitioning parameters, supported partitioning modes as well as a descriptions of log files, sequence output files and statistics files. It enables researchers to build a retrosynthetic roadmap for efficient manufacturing of genome-scale DNA designs.
An extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and homologous recombination. A cloning strategy expressed as a Pydna script provides a description that is complete, unambiguous and stable. Execution of the script automatically yields the sequence of the final molecule(s) and that of any intermediate constructs. Pydna has been designed to be understandable for biologists with limited programming skills by providing interfaces that are semantically similar to the description of molecular biology unit operations found in literature.
Simplifies the computational design of such synthetic biology parts. PartsGenie allows flexible design of multiple synthetic biology parts through the use of a simple web interface. Designs can be assembled through the arrangement of multiple features, which can be drag-and-dropped from a palette that include ribosome binding sites (RBSs), or coding DNA sequences (CDSs). It offers an integrated UniProt search tool, allowing sequences, NCBI Taxonomy terms and enzyme classification (EC) numbers to be automatically extracted and associated with the CDS, facilitating future traceability.
Allows modular assembly of Golden Gate-compatible cloning broad-host range vectors from a library of vector parts. BEVA is useful for the construction of new bacterial vectors, for cloning and gene expression in R. It allows researchers to simplify the genetical manipulations. This assembler is based on the Type IIS restriction enzyme Esp3I. It can serve for low copy number stable vectors for stable environmental gene expression in environmental samples where no antibiotic selection is applied.
Provides the industry with a comprehensive platform for all your synthetic biology needs. You will benefit from direct connections to an array of DNA synthesis providers, lab facility services and an extensive suite of advanced bio-informatics tools and genetic repositories, all in one platform.
Allows users to work on DNA sequences. WebDSV assists in creation, edition and analysis of DNA sequences. This tool enables visualization of sequences and permits user to mark them. It generates plasmid maps and saves user work in different files (fasta or GenBank format).
Provides an integrated construction design interface to facilitate building construction for all levels of experience. GenSmart™ Design is a web application that can automatically annotate DNA sequence and draw free plasmid map. Users can archive design securely for future use. This online resource includes automatic error-checking in all steps of the process.
A molecular biology program for DNA analysis, assembly and cloning. Built by scientists for scientists, its goal is to be exceedingly user-friendly and intuitive, while making no sacrifices in functionality and incorporating all necessary functions in a single application.