The science of today is the technology of tomorrow! And we believe that tomorrow has arrived now! With the establishment of separate course named Bioinformatics, we have entered into a new era of learning.
Hello fellow scientists! Are you stuck in one of your Biosciences projects that requires substantial computational analysis? Or are you on the verge of breakthrough discovery? The thought of choosing the right Bioinformatics software haunting you? Then you have arrived at the right piece of writing.
In this review article, I bring you a review of Geneious, a widely known Bioinformatics software. This Geneious review shall cover all the aspects of this software like what the tool is all about. Why should it be used and why it shouldn’t. Is it cost-effective or not, and my final thoughts about it.
Keep reading on until you find all the answers to your biological puzzle.
Geneious: What this Software is all about?
Geneious software is a biological analysis software created in Java Swing. The rate of interoperability is significantly high due to this among all commonly used Operating systems.
The Geneious software allows extensive visualization, manipulation, and transfer of DNA of all types like circular, straight, oligos, etc. along with peptide chains, multiple alignments, phylogenetic trees, contig assemblies, statistical graphs, 3D structures, chromatograms, and electropherograms.
The list is endless. If you wish to know the countless features, keep reading the upcoming sections.
9 Key Features of Geneious- What it offers?
Geneious is a platform for scientific amalgamation of molecular biology, genetics, and computational applications. It performs tasks of analysis via a simple user interface. Some of the highlight key features include:
 Next-Generation Sequencing Assembly and Analysis
One of the most important molecular analysis is NGS technology. With the help of the Geneious tool, data can be imported in a wide range of formats. After data import, the pre-processing takes place.
The reference mapping and de novo assembly are flexible. Bowtie and Velvet options are available on Geneious Server for analysis of NGS data.
 Visualizations and Graphics
The 3 Dimensional structures can be visualized briefly with proper labels. The sequence, alignments, assemblies, annotations, and restriction sites can be visualized.
The secondary structure of RNA can be visualized too. The construction of phylogenetic trees, dot plots, and virtual gels are possible via Geneious software.
 Editing and Assembly of Chromatogram
The Sanger sequencing data is assembled on the chromatogram. The Sequencher data is imported from .CAF file. The assembly of sequences takes place in order of their name. It is also possible to call the secondary peaks on this tool.
 Alignment and Phylogenetics
The sequence alignment features are exhibited by this software. All the major alignment algorithms such as MUSCLE, MAFFT, MAUVE genome, translation, and profile alignments can be executed. ClustalW which is also a type of alignment algorithm is embedded to it.
The phylogenetic involves the study of evolutionary relationships. Trees such as Neighbourhood Joining (NJ), UPGMA, PhyML, etc can be constructed. Bootstrapping and consensus trees development choices are also provided. The tree viewing is in interactive mode.
It is a one-step process for multi-site Gateway cloning. One-step for inserting the fragment of DNA into the vector. The virtual gel viewer is enabled for viewing the process. The restriction digestion is executed too. It shows the non-cutting enzymes.
 Database Exploration
The biological databases available on different platforms can be retrieved on Geneious. The literature search, sequence search, local search, and automated searching agents can be employed on the software. General BLAST and custom BLAST searches such as protein-protein BLAST, DNA-DNA BLAST, protein-DNA BLAST, etc. can be executed too.
 Primer Design
The PCR primers and probes for the process of amplification can be designed here. The software has an in-built PCR primer database. You can choose the primer as per your requirement by testing the Primer to the sequence. However, the sequencing and multiplex primers are yet to be launched on the platform.
 Prediction and Manipulation
The secondary structures of protein can be predicted. Sequences such as ORFs, repeats, and CpG islands can be known. Besides these, the cleavage sites and transcription factors can be identified. The Antigenic regions, Pfam domains of the protein structure, SNPs, INDELS, coverage can be interpreted and annotated.
 Biocode LIMS
It manages the sequences in 96/384 well plates. It can import the chromatograms and attach them to the well plates. The bin and trim of chromatograms if followed after the attachment process. The Taxonomy and Genbank can be verified. It allows Genbank submission as well.
The parameter to define the goodness of any software is the quality of output. Here we have a short yet appropriate description of one of the mapping tools.
The figure given below is the de novo assembly of the raw Oxford Nanopore and PacBio long read sequences. Using the plugin Flye both genome projects and metagenome assembly can be can be performed.
Here the Reference sequence is E.coli K12 MG1655 along the Mapper Minimap2. The data type is sensitive that is less than 5% divergence in results which is actually good.
Some significant papers with Geneious citations that recently got published are:
- Chong, Yoong Min, et al. “Complete Genome Sequences of SARS-CoV-2 Strains Detected in Malaysia.” Microbiology Resource Announcements, vol. 9, no. 20, 2020.
- Deng, Xianding, et al. “Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.” Science, June 2020
- Jaimes, Javier A., et al. “Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop.” Journal of Molecular Biology, vol. 432, no. 10, May 2020, pp. 3309–25
- Stefanelli, Paola, et al. “Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe.” Eurosurveillance, vol. 25, no. 13, Apr. 2020, p. 2000305
- Zehender, Gianguglielmo, et al. “Genomic characterization and phylogenetic analysis of SARS-COV-2 in Italy.” Journal of Medical Virology, vol. n/a, no. n/a, Mar. 2020
Some significant papers on RNAseq published by the help of Geneious tool are:
- Hidalgo-Cantabrana, Claudio, et al. “Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus.” Proceedings of the National Academy of Sciences, vol. 116, no. 32, Aug. 2019, p. 15774
- Brettell, Laura E., et al. “RNAseq Analysis Reveals Virus Diversity within Hawaiian Apiary Insect Communities.” Viruses, vol. 11, no. 5, May 2019, p. 397
- Alcolea, Pedro J., et al. “RNA-seq analysis reveals differences in transcript abundance between cultured and sand fly-derived Leishmania infantum promastigotes.” Parasitology International, vol. 67, no. 4, Aug. 2018, pp. 476–80
You must read these articles to know the participation of the tool in developing significant results.
This part can be tricky. You might be considerate before spending money on something like this, provided there is countless free software available too. Geneious software can be availed by users with different subscription values.
First of all, you should understand if you want to buy the program and use it. I hope the key features sections helped you go through the reasons. Nevertheless, you can go for the free trial version of 14 days before subscribing to any of the packages.
The subscription has been divided into two categories. They type one is Personal Subscriptions and type 2 is Group Subscriptions. The two will be discussed in detail now.
1. Personal Subscriptions
It involves downloading of the software on one machine only. In case of two devices, only one device would run the application at a time. It includes 3 types of plans:
Student Personal Subscription– A very basic plan for any student enrolled in an active degree program with key interest lying in Bioinformatics. The active support and automatic upgrades are available. It can be purchased online only. The cost of this subscription is $200 per year or $16.66 every month.
Academic Personal Subscription- This subscription plan is specifically for academic, governmental and non-profit organizations. The active support and automatic upgrades are available. The cost of this subscription is $450 per year or $37.5 per month.
Corporate Personal Subscription– This subscription is for the Commercial industries and profit organizations. It extends active support and automatic updates. The cost for this subscription is $1500 per year or $125 per month.
2. Group Subscriptions
More than one individuals can buys a plan together. New users can be added with any previously bought group subscription. It includes 2 types of plans:
Academic group Subscription– The minimum seat for this is 2. The educational, government and non-profit organizations can avail the services under this plan. The cost is around $450 per seat per year. The number of seats can be added at a prorated rate. The active support and automatic upgrades are available.
Corporate group Subscription– The minimum seat for this is 2. The commercial and profit organizations can avail the services under this plan. The cost is around $1500 per seat per year. The number of seats can be added at a prorated rate. The active support and automatic upgrades are available.
Go for the trial version first. See if it meets the needs of your labs and research. If it does, give it another serious thought and then buy.
Pros and Cons of Geneious Bioinformatics Software
Geneious can be considered as prima facie tool for initial studies of an unknown sequence. Some advantages that makes it unique are mentioned below:
- A good choice to carry out the Sequence Analysis and Genomics study.
- User-friendly with an intuitive interface
- Essential genomic tools are embedded for NGS, Sanger, and long-read sequence analysis
- Allows multiple and pairwise alignments, de novo assembly, mapping, visualization, annotation, prediction, and phylogenetic analysis
- It can perform primer designing and cloning operations
- Annotation of plasmid maps and vectors
- Finds CRISPR sites and codon optimization
- Management of data
- Simple drag and drop options
- Import and export and conversion of sequences and annotations
- Supported by Mac, Windows, and Linux platforms
- Additional benefits: Automatic workflows, Avail the Geneious Server database for data security, add plugins to increase the functionality
Geneious has thousands of citations yet it has some drawbacks that you must consider before jumping on any conclusions. These disadvantages are mentioned below:
- Yes, the price can be a bit too much for what it provides
- Upgradation can cost more money in the subsequent years of subscription
- Time duration for obtaining analysis outputs can be longer
Most of the Bioinformatical tools are often complained about for the difficult user interface. However, the case may be different in some software like Geneious that uses a click interface instead of command-line.
Geneious is certainly designed for easy usage. Single-button clicks makes it much more intriguing. The software is user-friendly, without a speck of doubt. However, the time taken to generate results for the analysis might be longer than usual due to congestion.
The step-wise tutorials and guide make the process of data retrieval, processing, and analysis easy peasy for the users. The guide videos for beginners is also provided. The Customer support seems promising. The next section includes how the Customer Support system of Geneious works.
I think the user-friendliness comes from the excellent Customer Support system. It feels like there is nothing to worry about once you start exploiting the tools.
There is a whole load of tutorials with data for step-wise understanding. There is a user manual that guides through every inch of the application. The videos and handbooks for understanding the software are mesmerizing.
There is a community of users who can take questions from other users. It is also called as Plugin Development Forum. Contact support is provided via email. You can directly contact the developers for any queries and assistance.
Limitations of The Software
Geneious is truly a genius in its way. It has settled most of our problems by providing all analysis quests at a single platform. However, some of the limitations that have come into the picture include the following:
- Some users are struggling with trial version. All the analysis options are not live in the free trial version.
- Some face issues while designing the primer. There are limitations
- People use BioEdit software, a free and easy to use sequence analysis application to overcome these limitations
- For general alignment, BLAST is the best choice
This article contains articulate analysis about the Bioinformatical software Geneious. The aspects of Features, Pros & Cons, Price, User support etc. was covered briefly. The functionality and major domains of scientific fields have been discussed too. In conclusion, I would like to summarize the article with some key points:
- Software is online
- Easily available
- Easy to understand interface
- Cost effective
- Accurate results
- Clear visualization
- Statistical graphs
- Fast and precise NGS workflow
- PCR and probe design
- Phylogenetic analysis
- Database search
- Price can be burdening
- Time for calculations might be longer
- Data can be stored in server but security remains a big question
- Extra charge for version upgradation might be asked for
Considering all the above points, I would recommend you try this tool at least once. You can undergo a trial period of 14 days. Go ahead only when you find it reasonable and worth the price.
It happens very rarely that a platform comes with so many integrated tools with the choice to add more plugins for additional functionalities. But it is also unavoidable that it comes with some drawbacks too.
Given below are the FAQs that relate to the Geneious software. Go through them once in case you have doubts.
Frequently Asked Questions
How do I renew my existing subscription?
- Select your plan of choice
- Enter previous license key
- Fill payment information
- Subscription is renewed
What is the difference between a personal and a group plan?
A group plan is for the team. The number of seats is equal to the number of machines which install the software.
A personal plan is for one person only. The software can be downloaded on two devices but only one device runs the software at a time.
How do I buy a student plan?
By availing the Geneious Prime student subscription, not through Purchase Order
Am I eligible for student pricing?
Only individuals enrolled for undergraduate and postgraduate courses can apply for this plan. A student license is allocated to student buyers.
What happens when my subscription expires?
The Geneious Prime subscription reverts to restricted mode on expiration. Most of the functions are disabled, though file import export is allowed. Data can be visualized too.
What support is offered?
Multiple tutorials and resources for step by step learning are available. On availing the Geneious Prime subscription, access to the scientific support team is also granted.