DNASTAR SeqBuilder Pro Review

Sequence analysis is a crucial step for any genomic investigation. Hence, to analyze a DNA or RNA or Protein sequence accurately, a reliable Bioinformatical tool is needed.

Are you thinking about using SeqBuilder Pro for your next notable scientific advance? Here are a few things that you must know about this Bioinformatical tool before going into buying it.

In this SeqBuilder Pro review, I bring you my opinions about the application. You shall find a lot about its usage, methodology, and pricing. Finally, I will tell you if the application is worth a try in the last section.

DNASTAR SeqBuilder Pro Review Software for Sequence Analysis

What Is SeqBuilder Pro Software by DNASTAR?

SeqBuilder Pro is a DNASTAR software developed by USA Company like DNASTAR Lasergene. It comes under the Lasergene Molecular Biology package.

SeqBuilder is particularly designed for some defined set of tasks. One could say that it is a macromolecular sequence analysis based program.

It is a commercial Bioinformatical product built for the scientific community all around the world. So far more than 67,000 customers have shown their trust in them. I expect more customers to become a part of this in the future.

However, a little deeper insight into the software’s abilities would let us know if it is worth the price. Let’s talk about the key features of the software in the upcoming section.

 

Key Features of SeqBuilder Pro

The SeqBuilder Pro package is a small part of the Lasergene Molecular Biology package, but it comprises the basic sequence analysis tools. Some key features or programs executed by the software include:

[1] Sequence Editing and Annotation 

A powerful feature of the SeqBuilder Pro for sequence analysis. Sequence editing and annotation is a primary step for molecular biology research. You can utilize this comprehensive editing software for change in sequences.

It provides the ability to change the nucleotides, amino acids, ORF identification, and addition of restriction sites. The process is automatic and the steps are simple. The editing can be done fast due to this.

1 Sequence editing and annotation
Image Source: DNASTAR

[2] Primer Design for PCR 

A perfectly designed primer is the key to setting up successful PCR experiments. However, any error in the initial step of Primer designing can ruin the entire setup.

SeqBuilder Pro provides this unique ability to design a virtual primer before performing the PCR in wet labs. The choice of editing primer through customization, editing, and mutating is beneficial. Even the first time users can rely on this for saving time and resources.

2 Primer Design for PCR
Image Source: DNASTAR

[3] Automatic Virtual Cloning 

Before trying your hands at the lab with clone designing, you need to know what the clone would be like. SeqBuilder Pro offers the flexibility to meet the experiment requirements.

The ability to batch clone groups of fragments simultaneously is possible here. The step-by-step guide helps in preparing the vectors and amplifying the inserts by different cloning methods (Gateway, multisite, GeneArt, TA, and TOPO).

3 Automatic Virtual Cloning
Image Source: DNASTAR

[4] Clone Sequence Verification 

After you have created a clone in your lab, you must validate your results whether it was done appropriately or not. The clone verification protocol by SeqBuilder Pro checks the correct orientation of the insert, adequate coverage of trace files, etc.

The identified discrepancies are immediately addressed by it. The workflow of verification catches the read misalignments and errors in insertions before moving towards the downstream experiments.

4 Clone Sequence Verification
Image Source: DNASTAR

[5] Plasmid Maps 

An interesting feature of SeqBuilder Pro is to offer an easy interface to create and annotate graphically rich maps for cloning and publication. There is an in-built tool for automatic annotation of plasmid using database features.

The software provides custom vector catalogs that provide annotated plasmid vector maps for in silico cloning.

5 Plasmid maps SeqBuilder Pro review
Image Source: DNASTAR

[6] Gel Electrophoresis Simulation 

This is a unique feature. The virtual gel electrophoresis in SeqBuilder Pro is amazing. You can apply the restriction enzymes to one or more DNA sequences to generate fragments.

This gel electrophoresis simulation can help you to easily determine the amount of agarose gel and markers required to segregate the DNA fragments.

6 Gel Electrophoresis Simulation
Image Source: DNASTAR

Technical Needs

The technical needs for all the DNASTAR products are the same. You need the following:

For Windows: 64- bit Windows 7, 8.1, and 10. The minimum RAM size is 4GB. The hard disk space of at least 400 MB is needed. A good internet connection would be appreciated.

For Mac: The version 10.13, 10.14, and 10.15 are required. The minimum RAM size is 4 GB. You can expand it depending on the size of data you wish to analyze. The hard disk space of at least 520 MB is needed. Try to get a good internet connection for smooth functioning.

For more details on the Technical needs, you can read the article on DNASTAR Lasergene.

 

Performance Analysis

SeqBuilder Pro has been cited several times in published research papers. Almost around 67,000 times.

Given below are the important researches that mentioned DNASTAR SeqBuilder Pro in the citations.

  1. In vitrostudies identify a low replication phenotype for hepatitis B virus genotype H generally associated with occult HBV and less severe liver disease In this study, the clones were made by inserting the 1.3 mer HBV sequence into EcoRV site of the vector pUC57. The verification of these developed clones was performed on SeqBuilder Pro and Editseq program of DNASTAR. Only after validation that the clones were perfect for further analysis the later steps were carried on.
  2. Endogenous melatonin promotes rhythmic recruitment of neutrophils toward an injury in zebrafish
  3. Dual ifgMosaic: A Versatile Method for Multispectral and Combinatorial Mosaic Gene-Function Analysis
  4. In VitroStudies Show that Sequence Variability Contributes to Marked Variation in Hepatitis B Virus Replication, Protein Expression, and Function Observed across Genotypes
  5. Systematic evasion of the restriction-modification barrier in bacteria
  6. Expression of Omp16 and L7/L12 Brucella abortus protective antigens as secretory fusion proteins in mammalian cells
  7. Non-canonical Helitrons in Fusarium oxysporum

 

Pricing Packages

This software comes under the Lasergene Molecular Biology package. The pricing of the Lasergene Molecular Biology package is divided into the following three categories:

  1. Lasergene Student Licenses: The annual license costs $300 for Lasergene Molecular Biology. The price for only SeqBuilder Pro is expected to be around $150 annually.
  2. Lasergene Academic Pricing: The annual license costs $249.
  3. Lasergene Commercial Pricing: The annual license costs $599.

Before buying the subscription, you can go for the 14 day free trial version. There is no obligation to buy even after free trial period is over.

For more details on pricing of DNASTAR software, read the article on DNASTAR Lasergene software.

 

Pros & Cons of SeqBuilder Pro

The PROS

SeqBuilder Pro has a very bright side. The tools accessed by the Bioinformaticians are a great help in the computational biology researches. Here are a few advantages of the software:

  • Comprehensive software for sequence editing that allows to easily carry out the editing process
  • Primer designing is accurate and editable
  • Plasmids can be mapped, annotated and compared
  • Simulate gel electrophoresis can run
  • Amount of agarose and markers can be known before performing in labs
  • Clone sequence can be identified and verified easily
  • Virtual cloning is possible
  • Sequences can be annotated, edited and mutated
  • The price is worth the services provided
  • The result accuracy and precision is commendable
  • High number of citations
  • Fast output generation hence, time saved
  • User friendly due to comprehensible user interface
  • Easy to interpret the output results
  • Inferences can be drawn easily
  • Publication ready images and graphs are generated
  • User guides, tutorials, webinars are available for guidance
  • Step by step videos for understanding the process of doing the research
  • Immense support from technical team
  • Easy to contact and deliver the problems to developers
  • 14 days free trial version before buying the product

The CONS

Every software has some loopholes hence a newer version is launched after a few days. Presently, SeqBuilder Pro might not be a complete package for sequence analysis. It lacks few features which you can read about in the “Limitations” section. Here is a list of disadvantages:

  • The price can be too much for what it offers
  • The software upgradation can ask for more money after a period of one year
  • The limitations can be a major obstacle for people reluctant to buy it
  • SeqBuilder is just for sequence analysis though a research can need more than just that. Hence, more features must be included
  • The size of the file can be huge so the result generation can take longer time
  • The efficiency of the tool can be questioned that is how well it produces results for different types of DNA/RNA sequences

 

User Experience

For any Bioinformatical tool to be great, it has to be embedded with the features of user-friendliness. In SeqBuilder Pro, this criteria of positive user experience is fulfilled. Here’s why:

  • The simple and comprehensible user interface allows any beginner level user to utilise the tools easily. The simple click options and OK options let the user feel less pressurized about the workflow or protocol.
  • The process of installation and configuration is simple Just install and you are ready to use the application for sequence analysis.
  • The process of license renewals and buying subscription is totally safe and secure. It is a hustle free process.
  • Bioinformatical tools only appear to be difficult. But actually, the SeqBuilder Pro software provides user guides, tutorials and webinars to the customers. This is a great initiative for the customer support to make the process of understanding the application supremely easy.

You might want to visit this link for the SeqBuilder Pro User Guide.

 

Customer Support

The application developers are very supportive as far as the customers and their problems are concerned.

  • User queries and doubts about the program functions are addressed immediately by the technical team.
  • The support team provides an email address to the user for asking questions.
  • The users can connect to a community of other users to discuss problems on a common platform.
  • The Lasergene Molecular Biology provides access to Tutorials. If you want to see them Click here.

 

Limitations of The Software

There are countless beneficial features of this sequencing and annotating program. However, it lags in a few aspects. You might consider these points while making a purchase for it.

  • SeqBuilder Pro does not allow to align sequences to one another or to a template. For the assembly of paired sequences to a reference you would need another software called SeqMan Ultra which is the part of Molecular biology package. This software supports SCF2 and SCF3 files.
  • No maximum upper limit of DNA sequence file size is known. If you wish to upload a huge size file, it is unsure if it would be accepted.
  • SeqBuilder Pro can’t design bulk set of sequencing primers for Sanger project. The functionality of picking primers every 500 base pairs for double stranded sequencing is not available at the present. However, such changes can be brought in the future.
  • SeqBuilder Pro does not support the real-time PCR primer designing. It does not have the protocols that are fully optimized for qPCR Probe design. However, there are underlying parameters to optimize such as Tm, Ta, GC content, secondary structure, and identification for false binding sites.

 

Wrapping Up

SeqBuilder Pro is an appropriate tool for various types of sequence analysis. Tasks such as primer designing, clone verification, gel electrophoresis simulation etc. can be performed with ease. Looking at the various positive as well as negative aspects, I would recommend you to get the DNA Lasergene package as a whole.

However, if you are at the basic stage of learning bioinformatical tools then you can go for SeqBuilder Pro software. Buying the software individually can be a costly affair. If your research demands for complete molecular and genetic level analysis, you must opt for entire tool package.

Buy only when it fits in accordance with your research requirements. Kindly visit the official website for detailed information.

 

Frequently Asked Questions

Can SeqBuilder Pro find gaps in a sequence?

Yes, it is possible to find gaps. Go on the option Edit. Click on Edit, click on Go to position. Type the desired location you wish to see on the sequence. Click OK. You would reach the specified position instantly.

Can I use SeqBuilder Pro to compare two plasmid sequences so that I can annotate various elements to show similarities and differences?

Yes, it is possible to do such comparisons between two plasmids. This can be done by clicking SeqBuilder Pro’s “Clone sequence verification” system.

Can SeqBuilder Pro quickly identify an ORF that meets various criteria and then save ORF as a new file?

You can rapidly search for ORFs on the SeqBuilder Pro application. You can specify your criteria for search.

Is there a way to change ‘U’ residues to ‘T’ residues in mRNA sequences without much delay or automatically?

Presently at the moment, there is no such option to replace the residues. However, with the release of Lasergene version 17.1 the choice to toggle between the sequences types DNA to RNA will become feasible. Hence all the ‘U’ residues would change to ‘T’ residues.

Is there a provision to remove the introns from the DNA sequence while viewing the RNA sequence?

No such facility is provided by the SeqBuilder Pro so far. Probably in the future, the upgraded versions would include this change.

Is there “lock” option to prevent any editing while navigating or viewing the sequence?

There is no such facility to “lock” the editing has been provided so far in SeqBuilder Pro. However, the SeqMan Ultra does provide this choice.

Is there any size limit to the DNA sequence file that can be opened on SeqBuilder Pro?

The capacity to load huge files is possible on this software. For example the Human chromosome 1 with 249 million base pairs in size opens and is fully annotated.

How to edit and make the primers functional? What are the criteria for designing good primers?

The User Guide by SeqBuilder Pro for primer related topics and videos can help in understanding the parameter for designing primers. The automatic detection of the non-optimal primers is made beforehand. The options to edit the primers and codons is available for optimal designing.

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