The Gene Construction Kit (GCK) program - Plasmid mapping software

The Gene Construction Kit® (GCK) program has been the preferred plasmid mapping software of leading researchers for more than 20 years. GCK allows easy manipulation of DNA sequences, either graphically or as sequence text - quickly saving users both time and money. GCK eliminates tedious examination of DNA sequence data by automatically identifying open reading frames (ORF's), keeping track of sticky ends during cutting and pasting of restriction enzyme digestion fragments, assisting with PCR primer design, and enabling comprehensive annotation of DNA sequence features. This DNA analysis software allows multiple files to be opened and displayed simultaneously, allowing DNA sequences to easily be copied and pasted between plasmids and vectors to represent real-world DNA cloning protocols. The Gene Construction Kit software is available for both Windows and Macintosh users, and files can be shared across platforms allowing for easy collaboration. The interface and set of functions in GCK will significantly enhance laboratory productivity and minimize experimental design errors - saving users both time and money.

Software Link: The Gene Construction Kit  (GCK) program - Plasmid mapping software

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Redasoft Visual Cloning - Cloning Plasmid Map designing Software

Draw Catalog Quality Maps and Design Cloning Experiments

- Restriction Analysis
- Restriction, TA & Gateway Cloning Experiments
- Export Images in Vector & Raster Graphic Format
- Draw Catalog Quality Plasmid Maps with MCS support
- Apply Custom Fonts & Themes

Software Link: Redasoft Visual Cloning - Cloning Plasmid Map designing Software

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NetPlasmid PLUS - Vector maps designing software

A simple yet powerful tool to draw your vector maps on the fly and over all your lab network!

Main Features of NetPlasmid PLUS:
- Integrates into LabCollector
- Very fast draw method
- Colored maps
- Network based
- Share maps over the lab network
- Save plasmid map images
- Edit plasmid maps
- Create empty vector maps
- Use and clone an Insert into a vector
- Insert values automatically update plasmid features
- and more ...

You can use NetPlasmid PLUS as stand-alone software in your lab or the one embedded in LabCollector. Both are identical.

Detailed Pricing

€500 for commercial users €250 for academic users 

Software Link: NetPlasmid PLUS - Vector maps designing software 

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Vector NTI - Sequence analysis software

Vector NTI® Advance software is the most highly integrated, multifunctional desktop sequence analysis application suite available today and provides superior integration, data management, and scalability.

Details

Vector NTI Advance® offers unparalleled, multi-modular, integrated sequence analysis and data management tools. The software contains a comprehensive set of data analysis and management tools, implemented across five application modules.

Detailed Pricing

$4,995 for a commercial license $2,998 for an academic license 

 

Software Link: Vector NTI - Sequence analysis software

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Drug Model Explorer - Clinical Research Software

DMX® is a software visualization and communication tool to explore model-based results of your compound?s product profile. Through the DMX interface you and your development team colleagues can address key strategic development questions by comparing probabilistic outcomes for different endpoints, treatment strategies, patient populations, and competing products.

DMX results are presented as a series of plots, tables and summary visualizations of predicted success" against performance targets that collectively define a product profile. DMX outputs can be quickly updated based on pre-simulated models of clinical effect. Results are accessible from networked desktop or laptop computers for individual exploration

Software Link : Drug Model Explorer - Clinical Research Software

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SimVector - DNA Cloning designing Software

An exceptional tool for drawing publication and vector catalog quality plasmid maps, carrying out restriction analysis and designing cloning experiments.

Draw Exceptional Publication Quality Plasmid Maps

Whether you are a catalog company selling engineered plasmids or are performing restriction analysis for recombinant cloning experiments, SimVector will help you simulate the experiments and create publication quality plasmid maps from start to finish. Use the software to draw circular and linear plasmid maps in a variety of colors, patterns, fonts and line types. Display enzyme names in two font styles with the bacterium portion in Italics, as is traditional. Use even more than one font style and color in a single textual word anywhere in the plasmid map including in the feature annotations.

Export plasmid maps in EPS format for Adobe Illustrator 10, SVG for Microsoft Power Point 2002 or as ready-to-host web pages. Choose JPEG, TIFF and PNG formats for export.

Multiple Cloning Site (MCS) Display is Unique to SimVector

Vector catalogs generally display MCS's in a unique format, with enzymes one above the other in a vertical list. SimVector identifies the MCS's by interpreting GenBank header annotations or you can specify them manually. It then draws them in this special format we call the "Bracket View". It even has the smarts to list only the enzymes that cut within the MCS and nowhere else..

Lightning Fast Cloning Simulation

SimVector transforms annotations in sequence headers from GenBank or local files into fully illustrated maps. The cloning wizard steps you through popular recombinant protocols, such as Gateway® cloning and TA cloning, as well as one and two enzyme restriction cloning. ORF search helps you ensure that the construct remains in-frame. With a click of a button, you can translate sequences of expressed proteins to check for possible reading frame errors. With SimVector, cloning simulation is as simple as clicking a few buttons.

Restriction Analysis

SimVector has a comprehensive restriction enzyme analysis functionality. Choose from a database of more than a thousand restriction enzymes or use a popular commercial enzyme set we have preloaded. SimVector also enables you to construct your own custom enzyme sets.

Biologist-designed Intuitive Interface

SimVector has an intuitive biologist-designed interface to perform restriction cloning and sequence analysis. Point-and- click wizards make it easy to use even for beginners, while versatile functionality offers full control to experts for drawing plasmid maps.

Software Link: SimVector - DNA Cloning designing Software

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Expression Primer - Primer Cloning designing Software

A revolutionary tagged primer design tool for designing expression cloning experiments

Extensive Assay Support for Tagged Primer design
Use the sophisticated algorithm of Xpression Primer to design thousands of tagged primers for expression cloning systems such as Gateway®, BD In-Fusion™, epitope and TOPO® Tools. You can choose to amplify an entire ORF or generate N terminal or C terminal fusion proteins. Xpression Primer ensures that the reading frame of the amplified ORF is conserved. To work with other expression systems, simply add functional tags of your choice and design tagged primers.

Successful Amplification with Nested PCR
To ensure the success of your PCR experiment, let Xpression Primer design nested tagged primers to amplify ORFs. You can locate the outer primers anywhere in the UTRs or in regions of no significant homology. Xpression Primer will BLAST your sequences, automatically interpret the results and design highly specific primers. The tagged inner primer pair amplifies the PCR product generated by the outer pair with little or no non-coding regions. You can also choose from a list of alternate primers to better meet specific experimental needs.

Sequencing for Product Verification Made Easy
The versatile algorithm of Xpression Primer can design optimal sequencing primers for multiple sequences in a single run. It picks forward primers across the amplicon at a specified interval and reverse primers staggered on the opposite strand. You can export the results for several popular well plate configurations.

Generate Precise Transcripts
Design primers to generate sense or antisense transcripts for in vitro expression studies.

Web Savvy
Xpression Primer searches Entrez and downloads batches of ORF sequences directly into the program.

Software Link : Expression Primer - Primer Cloning designing Software

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Expression Primer - Primer Cloning designing Software

A revolutionary tagged primer design tool for designing expression cloning experiments

Extensive Assay Support for Tagged Primer design
Use the sophisticated algorithm of Xpression Primer to design thousands of tagged primers for expression cloning systems such as Gateway®, BD In-Fusion™, epitope and TOPO® Tools. You can choose to amplify an entire ORF or generate N terminal or C terminal fusion proteins. Xpression Primer ensures that the reading frame of the amplified ORF is conserved. To work with other expression systems, simply add functional tags of your choice and design tagged primers.

Successful Amplification with Nested PCR
To ensure the success of your PCR experiment, let Xpression Primer design nested tagged primers to amplify ORFs. You can locate the outer primers anywhere in the UTRs or in regions of no significant homology. Xpression Primer will BLAST your sequences, automatically interpret the results and design highly specific primers. The tagged inner primer pair amplifies the PCR product generated by the outer pair with little or no non-coding regions. You can also choose from a list of alternate primers to better meet specific experimental needs.

Sequencing for Product Verification Made Easy
The versatile algorithm of Xpression Primer can design optimal sequencing primers for multiple sequences in a single run. It picks forward primers across the amplicon at a specified interval and reverse primers staggered on the opposite strand. You can export the results for several popular well plate configurations.

Generate Precise Transcripts
Design primers to generate sense or antisense transcripts for in vitro expression studies.

Web Savvy
Xpression Primer searches Entrez and downloads batches of ORF sequences directly into the program.

Software Link : Expression Primer - Primer Cloning designing Software

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QuickGene - Molecular Biology Software

QuickGene is a molecular biology program for DNA analysis, assembly and cloning. We scientists deserve decent, modern software that doesn't require manuals or training courses to learn to use and that's where QuickGene comes in.

Details
Introducing the world's first intelligent and friendly genetics software.

QuickGene is a molecular biology program for DNA analysis, assembly and cloning. We scientists deserve decent, modern software that doesn't require manuals or training courses to learn to use and that's where QuickGene comes in.

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.

regular updates keep QuickGene up-to-date
We're constantly working to make this a reality, introducing new features every month. QuickGene aims to be the absolute best while remaining affordable to everyone and constantly improving!

explore great new ways to create, visualize and share your research.
QuickGene already tackles all the basics of sequence analysis and introduces a number of great improvements.
The clean, tidy interface provides extensive sequence information exactly when and where you need it as well as offering the best search tool available. Fly through schematic sequence maps with navigation tools similar to those found in Google Maps and leave your enzyme catalogs on the shelf, as all restriction enzyme and buffer information is kept up-to-date!

save time & money with smart innovation
You can easily communicate your ideas from within QuickGene and we love to read and discuss every suggestion. Only with feedback will we be able to reach our goal of creating the best software to date with all the features you need. Your help is instrumental in this process!

Software Link: QuickGene - Molecular Biology Software 

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DNA Dynamo - Molecular Biology Software

DNADynamo sequence analysis software is easy to use. It's user interface is focused on your DNA sequences, proteins and restriction enzyme sites. Sequencing data, oligonucleotide sequences, DNA/Protein annotations and notes can be added to each sequence. Information is accessible whenever it is needed. The more you use the software the more useful your sequence files become as you accumulate notes, annotations, oligos and sequencing data. Suitable for molecular biologists at any level, use DNADynamo to plan your DNA cloning, draw high quality plasmid maps, analyse your dna sequencing data, blast search at ncbi, retrieve genbank files from entrez, assemble multiple sequence alignments, and much more
Details
DNADynamo sequence analysis software is easy to use. It's user interface is focused on your DNA sequences, proteins and restriction enzyme sites. Sequencing data, oligonucleotide sequences, DNA/Protein annotations and notes can be added to each sequence. Information is accessible whenever it is needed. The more you use the software the more useful your sequence files become as you accumulate notes, annotations, oligos and sequencing data. Suitable for molecular biologists at any level, use DNADynamo to plan your DNA cloning, draw high quality plasmid maps, analyse your dna sequencing data, blast search at ncbi, retrieve genbank files from entrez, assemble multiple sequence alignments, and much more. You won't need to read a long and complicated manual, and if you do have questions about how to use the software we are more than happy to answer them. DNADynamo bioinformatics software is available for Windows PCs including XP, Vista and Windows7, Macs running OS X 10.2.6 or later, including OSX 10.4 'Tiger', 10.5 'Leopard', 10.6 'Snow Leopard', 10.7 Lion, 'Intel and PPC' Macs', and Linux.

If you are looking for an alternative now that Vector NTI is no longer free, you might be interested to know that the DNADynamo demo can open VectorNTI database sequence files and import or export your DNA sequences and annotations as DNADynamo files, or genbank files, for use in other dna sequence analysis software.

Software link : DNA Dynamo - Molecular Biology Software

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