ArticleBMC bioinformatics2011
Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
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- In-silico design and evaluation of an epitope-based serotype-independent promising vaccine candidate for highly cross-reactive regions of pneumococcal surface protein A.Journal of translational medicine · 2023Article
- Identification of consensus hairpin loop structure among the negative sense subgenomic RNAs of SARS-CoV-2.Bulletin of the National Research Centre · 2023Article
- Asynchronous multi-decadal time-scale series of biotic and abiotic responses to precipitation during the last 1300 years.Scientific reports · 2020Article
- Stepwise optimization of recombinant protein production in Escherichia coli utilizing computational and experimental approaches.Applied microbiology and biotechnology · 2020Review
- Antibody signatures in patients with histopathologically defined multiple sclerosis patterns.Acta neuropathologica · 2020Article
- Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs.The Plant cell · 2020Article
- Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways.iScience · 2020Review
- Heterologous expression of biologically active Mambalgin-1 peptide as a new potential anticancer, using a PVX-based viral vector inPlant cell, tissue and organ culture · 2020Article
- The non-synonymous mutation in bovineHeliyon · 2019Article
- Improvement of Fab expression by screening combinatorial synonymous signal sequence libraries.Microbial cell factories · 2019Article
- A multi-method and structure-based in silico vaccine designing againstBioImpacts : BI · 2019Article
- Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions.Science signaling · 2018Article
- Chimeric Proteins Containing MAP-1 and Functional Domains of C4b-Binding Protein Reveal Strong Complement Inhibitory Capacities.Frontiers in immunology · 2018Article
- A novel B- and helper T-cell epitopes-based prophylactic vaccine againstBioImpacts : BI · 2018Article
- Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli.BMC bioinformatics · 2017Article
- Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins.Journal of genetics · 2016Article
- A new strategy to express the extracellular α-amylase from Pyrococcus furiosus in Bacillus amyloliquefaciens.Scientific reports · 2016Article
- Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs.Computational and structural biotechnology journal · 2016Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDirect gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer.
resultsThe software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment.
conclusionVisual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.