Sequencher Review – A DNA Sequence Analysis Tool

Recent advancements in biological scientific research indicate that how Bioinformatics tools like Geneious, DNASTAR Lasergene, Sequencher, etc. are a boon for the life science scientists. With new developments in the field of study each day, new methods of analysis and interpretation are the need. So are you looking for an appropriate DNA and RNA analysis tool?

In this Sequencher review article, I shall throw some light upon the Genecodes product known as Sequencher a Sequence analysis software. The various aspects of the software like how it works? What are the pricing, features, and drawbacks? Etc., would be discussed in details.

In the last section, you shall read about my final opinion on the software, if it is worth buying or not. My conclusions are established based on the particulars of this product.

Sequencher Review DNA Sequence Analysis Software

What is Sequencher?

Sequencher 5.4.6 is one of the Bioinformatical products by the Gene Codes Corporation. Another production by them is CodeLinker. Sequencher is software for sequence analysis for Sanger, NGS, and RNA-Seq.

Sequencher is presumed to be an all-in-one tool for the top scientists. It provides several features like reference guided alignments, SNP analyses, de novo assembly, etc.

The other subsidiary features- technical support, licensing, and tutorials are appreciated too. Let’s find out how well the software fits into these pre-defined notions in the upcoming sections.

 

Characteristic Features of Sequencher

Gene Codes has developed powerful tools for scientific insight in the past. With the development of Sequencher, the DNA sequence analysis and manipulations became possible. Here is a list that defines how good the application is:

[1] General Analysis

As the name suggests, this feature enables some general features. For example,

The “Customization of workspace”, lets you choose all the default options for your windows. You can choose all the settings for default and save the Reference sequence also.

Sequencher General Analysis
Image source: Gene Codes

Find amino acid” option in Sequencher helps in identification of amino acids within the data set. “The Variance table” helps in visualizing the bases and identification of regions of interest. ”Translated variance table” displays the matches and mismatches.

[2] Connections with Databases

This feature enables the multiple analyses on single or multiple sequences. Basic Local Search Alignment Tool (BLAST) can be performed on the single sequences. Primer-BLAST channels can be used to design primers and use them in Sequencher product.

These connection sessions are saved automatically. New sessions can be created, saved, reviewed, and run. Multiple sessions can be run at the same time. MUSCLE Alignment algorithm can be executed on a cluster of sequences. A Phylogram (tree) displays the alignment results.

Image source: Gene Codes

[3] Sanger Sequencing

This is the traditional method for sequencing. Sequencher provides this facility to perform it. The sequences can be trimmed, assembled to the reference sequence, automate the assembly by Assemble name, edit the data to deal with ambiguities.

Confidence values based data trimming, quality control, detection of Single Nucleotide Polymorphism etc., can be performed for result improvement. Overall the task performed here include:

  • Sequence editing, trimming, assembly
  • Assemble to reference
  • Multiple sequence alignment
  • Restriction mapping
  • SNPs detection
  • Automatic analysis
  • Confidence value based analysis

[4] Next Generation Sequencing

The latest method of DNA sequencing and high throughput data analysis is the NGS technology. It is not surprising that Sequencher provides accessibility to NGS analysis tools. The FastQC Quality Control reports can be obtained for any sequence data.

RNA-Seq NGS data can be aligned to a reference genome, the SAM and BAM file formats are obtained. A four step process- Cufflinks, Cuffmerge, Cuffdiff, and output in the form of tables and graphs identifies the differentially expressed genes.

Besides this, the process of de novo assembly, reference guided alignment, SNP Analysis, Methylation studies, Multiplex ID etc. can be studied.

 

Performance Analysis

Sequencher has been cited in more than thousand papers for its effective and proficient contribution. Given below is an example of the research analysis made with it.

Sequencher Review Performance Analysis
Image source: Research gate

This is a graphical representation is from a research paper titled “A high-throughput Sanger strategy for human mitochondrial genome sequencing”. This is mtGenome (mitochondrial genome) sequence coverage captured from Sequencher screen for coverage results from 135- sequence strategy. The green denotes the forward sequences and the red represents the reverse sequences. The blue hashing in the coverage bar and asterisks represent the small regions with replicate and unidirectional coverage.

There are many more scientific papers with similar type of sequence analysis that has gained global recognition. Due to this very reason, Gene Codes has been felicitated with awards from many organizations across the world. Some of the acknowledgements are:

  • Merlanti Prize
  • Indestructible award for Growth and Achievement
  • Washtenaw County Fast Track Award

 

Pricing

As per the Gene Code website, the price of one year license is $999. It is the same for all the organizations and individuals. One year of free maintenance and support is provided. Later years of licensing would include additional charge on maintenance and technical support.

The pricing can vary depending on the duration for which you buy the license. Depending on duration if it is a six month project or a twelve month project, money would be charged on license.

You can first go for the free trial version of 15 days followed by purchasing the entire product. There is no obligation in buying the license after trial period is over.

 

System Requirements

The technical needs are complicated so make them clear for once and all. Previous versions from Sequencher 4.10.1 do not get installed on any drivers on 64 bit operating systems. Only 64-bit compatible drivers are good to go with this.

1. Windows

  • Sequencher 4.8 and above versions are supported by Windows 7, 8, and 10.
  • The software requires a 64-bit processor. Sequencher 4.10.1 and above versions automatically install 64 bit drivers on 64 bit OS.
  • The minimum Hard disk space required for running Sequencher on Windows is 280 MB and minimum memory requirement is 3GB RAM.
  • Hard disk with minimum 580 MB free space is needed for running RNA-Seq and DNA-Seq data.
  • An additional 8 GB RAM is needed for DNA and RNA Seq data.
  • If you use GSNAP 16 GB RAM is recommended for smooth functioning.

2.  Mac

  • Sequencher 5.4.6 version is compatible with Mac 10.7, 10.8, 10.9, 10.10, 10.11, 10.12, 10.13, and 10.14.
  • The minimum Hard disk space for running Sequencher on Mac is 355 MB and memory requirement is 8 GB RAM.
  • An additional hard disk space of 320 MB is needed for running DNA-Seq and RNA-Seq tools.
  • For running GSNAP 16 GB RAM would be needed.

Hence, I would recommend you to have a hard disk of at least 1000 MB size and RAM of size 16 GB.

Note: Sequencher 5.4.6 is not compatible with macOS Catalina 10.15. Do not upgrade your Mac if you wish to continue to use Sequencher. Wait until Gene Code sends an email to you confirming the compatibility of Sequencher in the future.

For further details visit this site

 

Pros & Cons of Sequencher DNA Sequence Analysis Software

PROS

The advantages of Sequencher that makes it a worthwhile experience for the scientific community across the globe are mentioned below.

  • Sequencher connections can increase the speed of obtaining results. It happens so because multiple sequences or groups of sequences are analysed simultaneously at the same time.
  • Connection on Sequencher is flexible and customizable. New sequences can be added to the previously existing sessions.
  • Obtains the results fast and accurately with the most optimum algorithms
  • There is a wide choice in buying license. Go with the one that is ideal for your machine and project. Choose between Standalone, Shared Network or Institution wide site license.
  • Free maintenance program with the first year of purchase.
  • Technical support, trainings and guides available for first time users and frequent visitors too
  • Video tutorials are available for Sanger DNA sequencing, NGS, RNA-Seq and Sequencher Connections for single and mixed analysis.

CONS

Every great tool comes with some or the other drawbacks. Sequencher also lacks some of the features such as:

  • The compatibility issues are disturbing. You need to know about all the technical needs before installing the software. This can be tricky and problematic.
  • The speed of processing and output of results depends on the size of data file
  • License upgradation is extremely necessary for the smooth functioning. Without it you can’t save, import, export and execute tasks.
  • Sequencher maintenance and support charge after one year of licence.
  • Way more costly than other similar sequence analysis tools such as Geneious. Read our detailed review on Geneious here

 

User Experience

This domain of Sequencher is applauded by the community of biological researchers.

  • The ease in use of the software is commendable. The simple and click through interface makes it interactive and attractive.
  • The users feel comfortable while performing de novo assembly or reference guided alignment without using the command line.
  • Multiplex ID is assigned for barcoded data, hence easy inference.
  • The tools are unique and so they help in organizing the analysis and streamlining them.
  • The plots, charts, and graphics are publication quality ready. Hence can be used directly for publications without further processing
  • The tutorials and guide videos make the understanding of tools functionality easier.

 

Customer Support

The commercial Bioinformatical software is good at playing this part. There are several methods to reach out to them for any quality of assistance or help. Sequencher maintainers provide various contact methods for its users too.

If you have any queries regarding the product pricing, maintenance pricing, technical support, need a training specialist or a sales person to contact you, directly contact them through an online form. Fill it up, ask you query, submit, and it is done.

Otherwise, you can reach the Sequencher team via email at [email protected] for general information, and [email protected] for technical support.

You can also mail them at this address for queries. Contact number and Fax number are also available on the website.

 

Limitations of Sequencher

Sequencher has contributed greatly in the fields of genetics, forensics, microbiology, pathology, virology, systematics, bioinformatics, etc. However, it has some undeniable shortcomings. Some of them are mentioned here:

  • The popping up of error message “The Sequencher was unable to find a key. The program will run only in the demo” when you have purchased either of the licenses. The error arises since Sequencher is not able to obtain a license from either a hardware key attached to the system that runs the program or from a Sequencher License Server or Key Server network.
  • Another problematic consequence is the incompatibility of newer Sequencher versions with the older versions of Windows and Macintosh. Kindly go through the technical needs of the software before updating your devices.
  • More advanced researches are not possible here such as primer designing, Virtual cloning, simulation of PCR, and virtual Gel electrophoresis etc.
  • If Sequencher could include the advanced research and analysis for proteomics study too (protein based analysis for structure, sequence, molecular docking, simulations, drug discovery etc.), it would have been worth the price.

 

Final Thoughts

This Sequencher Review article includes all the major aspects of the software. The Features, Pros, Cons, pricing and limitations have been briefly described. Now we have reached the final section of this review article on Sequencher.

Here I would present my final thoughts on the software.

Looking at the positive outcomes of using the software and the enormous amount of data it has produced in the past, I would recommend you to give it a try.

The reason for this is that it is a complete package. Multiple types of sequence analysis for DNA Seq and RNA Seq data can be performed at a single platform. From performing BLAST to generating NGS data, you get all at one place at one time.

The only troubling part for this software is the affordability. It seems too expensive at $83.25 per month. It is an unfair deal for students who want to perform analysis on individual basis. Academic organisations rarely buy the tools for research and analysis due to various constraints.

To overcome this problem, you can rely on multiple open sources.  But the drawback with them is that you will have to go to multiple sites of Bioinformatical tools for your data analysis. Obtaining results at one place and saving the session for later use is not possible in open sources. The size of the file is also a concern. If it is too long or heavy, analysis might get inaccurate.

You can first go for the 15 days free trial version for Sequencher. It does not pose any obligations for purchasing in the future once the trial phase is over.

You can evaluate all the aspects of analysis and then decide if you want to buy it for your projects or not. Since the licensing options are flexible, it can be purchased as per your duration of need. You can cancel if it does not meet the expectations.

 

Frequently Asked Questions

What is the latest version of Sequencher?

The current version is Sequencher 5.4.6. It is Forensic enabled. Older version can be easily upgraded to the latest version.

Can I use Sequencher for a trial period?

Yes, you can use Sequencher for a 15 days trial period by downloading and installing Sequencher on your device. The free version comes with all the viable options. Try your own data on this for analysis.

How to configure Proxy settings?

Any change in proxy settings is auto detected by Sequencher. When there is a change or problem in Proxy settings, you will be asked to change the settings. Sequencher then uses the new settings.

What type of licenses are issued by Sequencher?

There are two types of licenses available. Standalone license (tied to a specific hardware key) and Network license (controls the number of users). Both the licenses are available as perpetual (does not expire and allows users to avail full functionality) or time limited (project licensed, expires soon).

Does Sequencher functions on Virtual machine?

Yes but only with KeyServer based license server not with standalone license. You can use with standalone license that is locked to hardware key.

How to get technical support for Sequencher?

It is easy to avail any technical support for Sequencher. The Customer support section includes all the contact details. You can reach out via email, phone number, fax, and mail. The maintenance charge is zero for the first year of subscription.

Does the license for Sequencher expire?

Yes, the license is perpetual. You can upgrade the license for latest versions.

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