MacVector - Molecular Biology Software

MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions. MacVector is widely regarded as the most intuitive, easy to use program available for sequence analysis.

Graphical Sequence Editing
MacVector can read and write DNA and Protein sequences in most popular file formats. In addition to directly editing sequences and features/annotations, MacVector has an intuitive "Click Cloning" graphical interface that lets you easily replicate laboratory cloning experiments to create new molecules. MacVector uses the native Mac OS X Quartz graphics to generate publication quality images that can be scaled to any size with no loss of resolution.

Gateway and Topo Cloning
MacVector supports the popular Gateway, TOPO TA and Zero Blunt cloning technologies from Invitrogen. With a few simple clicks from an intuitive graphical interface, you can replicate your biological manipulations at the bench to create new molecules with the correct sequences across the cloning and recombination junctions.

Auto Annotation
You can scan an unannotated or partially annotated sequence against a folder on your hard drive and MacVector will identify matching features in sequences in the target folder and add them to your sequence. Because MacVector includes custom feature appearance information when annotating the sequence, you can use this to maintain a carefully curated set of your favorite genes and sequences each with a graphical appearance that best suits your needs.

Primer Design
You can design primers for either PCR or Sequencing/Hybridization probes using the primer design functions. In addition, you can test specific primers to determine if they have secondary structure problems, alternate binding sites or other characteristics that might impact their use in experiments.

DNA Analysis
MacVector provides a wide variety of useful DNA analysis tools, including base composition analysis, Restriction Enzyme searches, DNA Subsequence searches and "Dot-Plot" comparisons between DNA:DNA and DNA:Protein sequences. A Coding Preference toolbox lets you select a variety of algorithms to graphically scan a DNA sequence for likely protein coding open reading frames.

Protein Analysis
Protein sequences can be reverse translated into DNA, compared using "Dot-Plot" analysis and scanned for Proteolytic cleavage sites and amino acid sequence motifs. A comprehensive Protein Analysis Toolbox provides a wide variety of algorithms for analyzing the composition of proteins and presenting the results in graphical and tabular formats.

Database Searching
MacVector has built-in Internet connectivity to the NCBI BLAST and Entrez databases. You can directly search Entrez for DNA or Protein sequences based on features, authors, keywords etc and directly download them into MacVector, complete with all features and annotations. The built-in BLAST interface lets you submit multiple BLAST jobs using DNA or Protein sequences and then download any matching sequences by selecting them from a hit list. Even without an Internet connection, MacVector can align sequences against any folder on your hard drive using a FastA algorithm, allowing for "local" database searches.

Multiple Sequence Alignment
You can align unlimited numbers of DNA or Protein sequences using the ClustalW algorithm built in to MacVector. A full-featured editor lets you make manual adjustments to the alignments and view them using a wide variety of customizable color schemes. You can create publication quality graphical outputs of the alignments and view pairwise combinations of the sequences in aligned and matrix formats.

Sequence Assembly
Sequence Assembly functionality in MacVector is now provided by two modules. First there is a built-in function called Align To Reference. This can be used for two different functions, Sequence Confirmation and cDNA Alignment. This is included with MacVector and allows you to import trace files or sequence files and assemble them against a template sequence. This is ideal for small scale sequencing projects, especially resequencing. For example, checking an in situ mutagenesis experiment, a construct you've just made, or confirming the sequence of a cloned PCR fragment. It's also an excellent tool for SNP analysis, with some special tools to allow you to easily spot mutations from your original template sequence.

For full scale sequencing projects where you do not know the sequence you'll need MacVector and a separately purchased plugin called Assembler. This is a full contig assembly application that uses the phred, phrap and cross_match algorithms from the University of Washington to assembles traces into contigs. It displays full quality scores of the reads and the aligned contigs. The trial version of MacVector also includes the Assembler plugin.

Software Link:  MacVector - Molecular Biology Software

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Primer Premier - Primer Design Software

A Comprehensive PCR Primer Design Software

Primer Design for Standard PCR Assays

Primer Premier is the most comprehensive software to design and analyze PCR primers.

Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor thermodynamic algorithm. Primers are screened for secondary structures, dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in ranked order. Equipped with a handy calculator, you can easily manipulate sequences and analyze the results of your primer design.

Load the gene of interest from NCBI, select a search range, sit back and let Primer Premier pick the best possible primers for you.

Primer Design for SNP Genotyping Assays

With Primer Premier, you can load sequences from dbSNP and have the primers designed flanking the SNP selected. Hundreds of unpublished SNPs can also be loaded by specifying them as variation features in standard GenBank/dbSNP files. After specifying the SNPs, primers can be designed to amplify them for detection using a probe-based chemistry.

Multiplex Primer Design

For a multiplex experiment, Primer Premier enables you to design multiplex primers by launching a primer search in batch mode and then checking the cross reactivity of the primers designed. Primer Premier checks for all the possible reactivity and displays the most stable structure formed by each oligo. This functionality reduces false priming and ensures a strong signal strength.

Automatic Homology & Template Structure Avoidance

Primer Premier automatically interprets the BLAST search results and avoids those regions to design primers that have significant cross homologies with the database. These homologous regions are highlighted in the sequence view and are avoided during primer search.

Primer extension may be hindered due to the presence of template structures at extension temperature. To avoid all such regions, where the template may fold upon itself, the program utilizes a proprietary algorithm to check for possible secondary structures within the template at a folding temperature you specify. The regions involved in the formation of a secondary structure are underlined in the sequence view and are avoided while designing primers.

Avoiding homologous regions makes the oligos highly specific and avoiding template structures improves the efficiency of the designed primers.

Manual Primer Search

Primer Premier offers complete control over primer design to the user. Using the manual primer search option, a user can select any position on the template sequence to design a sense or an anti-sense primer. Primer Premier instantly calculates and displays the properties of the new primers. The primers finally selected by a user are then shown in the Sequence View on the Main window.

Edit Template Sequence

The template sequence is editable and can be changed by a user. Bases can be modified using the standard Cut/Copy/Paste functions. Unwanted regions of sequences can be removed by using the Delete button. Users can comment or annotate a sequence and save them for future reference.

Software Link: Primer Premier -  Primer Design 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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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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PrimerPlex - PCR Oligo designing Software

Oligo Design for Multiplex PCR & High Throughput SNP Genotyping and Analysis

PrimerPlex is an efficient and sophisticated tool for designing oligos for multiplex assays. Multiplex assays facilitate amplification of multiple targets in a single reaction vessel, reducing both the time and cost of experimentation.

PrimerPlex designs oligos for multiplex PCR assays and for suspension array based systems such as Luminex 100, Luminex 200 and Bio-Plex 200. Such systems offer a versatile platform for multiplexed nucleic acid detection in a 96-well format. PrimerPlex designs specific capture probes for direct hybridization assays and primers for Allele Specific PCR Extension (ASPE) assays.

The multiplex assays are used for gene expression analysis (end point detection using gel electrophoresis) and for high throughput SNP applications such as genotyping, pathogen detection, strain typing, and haplotyping. To ensure specificity, the oligos are designed after avoiding the regions of homologies identified by a BLAST search. PrimerPlex then checks the oligos for cross reactivity and minimizes Tm mismatches to give you the best possible multiplex set. In the process, it analyzes millions of possible multiplex primer sets in a few seconds and presents a list of alternate sets to you as well.

Design Options

Multiplex PCR Primer Design
PrimerPlex designs standard primers for a 30-plex multiplex PCR assay. It uses proprietary algorithms to design optimal primer sets under uniform reaction conditions for up to 30 targets. Primer sets are identified after screening all the primers in a pool and minimizing Tm mismatches. All the multiplex primer sets are analyzed for cross hybridization to ensure specific amplification and high signal strength.


Direct Hybridization Assays

PrimerPlex designs optimal allele specific capture probes for high throughput SNP genotyping assays. The probes are designed such that the mutations are at their centers to maximize differentiation. Each one of the probes designed is checked for its suitability in a multiplex reaction. For amplifying the templates, the program designs SNP flanking primers as well. This functionality makes PrimerPlex the only software product capable of designing probes for 100 individual targets for a multiplex assay.


ASPE Assays

Another approach to detect mutations is to use a solution-based sequence specific enzymatic reaction such as Allele Specific Primer Extension (ASPE) to determine the target genotype. PrimerPlex designs highly specific primers for multiplexed ASPE assays. The ASPE primers are designed such that the mutations lies at their 3' end. PrimerPlex also designs primers to amplify the target sequence for ASPE assays.

Software Link : PrimerPlex - PCR Oligo designing Software

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Beacon Designer - PCR Primer designing Software

Automate your real time PCR primer and probe design
Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.

Specific and Efficient Design: How Beacon Designer™ Makes it Possible?

You can BLAST search sequences and search for template structures from within the program. The results of both these searches are used while designing primers and probes. The regions that exhibit significant cross homologies and template structures are avoided automatically during the design.

Design Options Available

• SYBR® Green Assay Design
• SYBR® Green is perhaps the most commonly used real time PCR chemistry. Beacon Designer™ designs
• SYBR® Green PCR primers and helps you evaluate pre-designed SYBR® Green PCR primer sets. 

You have complete control over the design parameters or you can use the default values, chosen after considerable research and communication with experts.

HRMA Assay Design
Beacon Designer™ offers a comprehensive solution for mutation detection. High Resolution Melting Analysis (HRMA) is a more cost-effective method than probe-based genotyping analysis. The program employs proprietary algorithms that enables designing the best primers for detecting mutations.

High Resolution Melting Analysis primers are designed flanking a mutation of interest to generate the shortest possible amplicons with detectable melting temperature variation. The primers are designed avoiding template secondary structures, assuring efficient primer extension. The HRMA primers designed can be BLAST searched against nucleotide databases at NCBI to check their specificity. Pre-designed or published primers can also be analyzed.

Dual Labeled Probe Design
Beacon Designer™ currently supports four probe based chemistries:

TaqMan® Probes
Use Beacon Designer™ for optimal TaqMan® probes that help you study the differential gene expression or study SNP (single nucleotide polymorphisms) using TaqMan® SNP genotyping assays. You can also choose to design the increasingly popular Locked Nucleic Acid (LNA™) substituted TaqMan® probes, which are more stable than standard TaqMan® probes. To study DNA methylation, Beacon Designer™ helps design primers and TaqMan® probes for MethyLight assays. MethyLight is a high throughput assay used to discriminate between methylated and unmethylated DNA. Using Beacon Designer™, you can design suitable control primers and probes by designing oligos for the methylated and the unmethylated strands, and for the untreated DNA sequence. With any of these chemistries, you could evaluate a pre-designed/published primers or TaqMan® probes. The design results are reported in a ranked order, giving you a list of alternates to choose from. Depending on the oligo properties, a rating is assigned. Please read the Rating section in the online help for details.

Molecular Beacons
Design or evaluate standard molecular beacons or molecular beacons for NASBA® assays. NASBA® is a primer-dependent technology that can be used for the continuous amplification of nucleic acids in a single mixture at one temperature. You can now design molecular beacons for NASBA® assays for single template or multiplex reactions.

Scorpions®
Beacon Designer™ supports the design of Scorpions® primers and probes. Scorpions® assays are important in that they are independent of the enzymatic cleavage of the probe. The primer and probe element are physically coupled during the reaction. Read more about the Scorpions® technology.

FRET Probes
Beacon Designer™ supports design and evaluation of pre-designed FRET probes. FRET probes that are compatible with pre-designed SYBR® Green primers can be designed in Beacon Designer™.
Multiplex Real Time PCR Assays

With Beacon Designer™ you can design TaqMan® based multiplex real time PCR assays for upto five sequences including reference gene selection.

Software Link : Beacon Designer - PCR Primer designing Software

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