Doing research in biology can be painstakingly slow, making it difficult to stay focused on the ultimate, most rewarding end goal: successful results. Oftentimes researchers are so engrossed in their projects that they forget the myriad resources available to them to help them be more efficient scientists. Ranging from visual aids to tools that predict things for you, the resources available for free online have been growing exponentially over the years and we believe scientists should take advantage. In this article, we synthesized and organized a list of online tools for molecular biologists. We think you will find it useful. Enjoy!
Pepinfo – a tool that creates plots to display info about amino acid properties. Examples include hydropathy and charged residues.
RBS Calculator – a design method used to help scientists predict translation initiation as well as protein expression specifically in bacteria. The calculator allows control over achieving a previously set translation initiation rate.
GeneMANIA – a comprehensive web interface that makes hypotheses about the function of specific genes or gene sets. The user inputs a gene list and this tool generates a list of functionally similar genes from desired data sets.
Cn3D (NCBI) – an application that allows users to view three-dimensional biological structures with ease. With data from NCBI’s Entrez Structure database, this application has myriad structures to analyze. Not only does it display structure, but sequence, alignment, and annotations are also displayed for users.
Virtual Ribosome – a tool that translates DNA sequences into the peptide sequences that match. It is able to use annotated sequences, which allows the tool to easily map introns/exons. Virtual Ribosome can calculate characteristics of the resulting peptides, including amino acid composition, molecular weight, and isoelectric point. It also has a built-in ORF Finder.
ZiFiT – a tool that identifies zinc finger nuclease sites within DNA sequences. This tool can be used to help identify CRISPR/Cas9 target sites as well as to actually construct the guide RNA.
MIT CRISPR Design Tool – a tool that finds off targets in a specified genome, determines guide sequences with target specificity, and also alerts users to guide sequences with many off targets.
CRISPR-P – a web tool that allows users to design single-guide RNAs for a variety of plant species. The tool provides a platform for users to search for specific Cas9 target sites on the DNA. Along with these functions, the tool provides off target site prediction as well as the marking of restriction enzyme cutting sites.
CHOP-CHOP – a tool that chooses the optimized site for CRISPR/Cas9 use given inputted data in the form of genes, genomic coordinates, and sequences.
NuPack – tool that predicts the secondary structure of each constituent and the interactions between different strands of RNA. It checks that, for example, the antisense and the probe don't dimerise without the signal sequence. The program does not have an algorithm to design secondary structure with specific nucleotide sequence.
Metabolic Pathways Tools
Reactome – a pathway database mainly used to provide visualization, interpretation, and analysis of different pathways. The information in the database is quality-assured and available in concise diagram and/or description form. For every reaction documented in the database, all of the molecules involved are identified and explained. The location of the reaction is also available.
KEGG: Kyoto Encyclopedia of Genes and Genomes – a database resource that provides information on high-level functions of different biological systems. Information of the cell, organism, and ecosystem is available. With data both at the molecular level and at the largest scale, this database is a comprehensive resource.
Primer 3 – a free, online tool that allows scientists to analyze and design primers for PCR and real time PCR. This tool can also be used to select single primers for sequencing reactions or to design oligonucleotide hybridization probes. It can be applied for variety of uses, namely to create sequence tag sites, to amplify sequences for single nucleotide polymorphism discovery, or for radiation hybrid mapping.
WebOligoMelt – easily and simply calculates melting temperature of an oligonucleotide.
NEBaseChanger – tool to design primers for site-directed mutagenesis experiments using the Q5 Site-Directed Mutagenesis Kit. The tool provides users with primer sequences, optimal annealing temperatures for PCR, buffer concentration, as well as the ideal primer concentration.
Webcutter – this tool helps restriction map nucleotide sequences. It also allows users to find sights that have possibly been introduced by silent mutagens and analyze sequences with ambiguous nucleotides.
Blast (NCBI) – an algorithm used to compare biological sequence information from a database. The tool can be used to compare amino acids of proteins or nucleotide sequences of DNA across the spectrum of life. It finds regions of similarity between biological sequences and then calculates the statistical significance of the similarity.
Clustal Omega – a DNA/RNA/protein sequence alignment tool. It can only be used for three or more sequences.
Multiple Alignment using Fast Fourier Transform (MAFFT) – a tool that provides multiple sequence alignment for amino acid and nucleotide sequences.
At Genome Compiler, we pride ourselves on our all-in-one design platform for myriad uses. In addition to many other tools not mentioned in this list, we have worked to integrate several of these existing tools in our software so that our users can be more efficient and organized. Having all of these tools on one platform rather than having to grapple with many different resources provides concise, clean, and quicker functionality for our users that are busy expanding the reaches of science. Genome Compiler combines the functions of Restriction Mapper, Virtual Ribosome, WebOligoMelt, Webcutter, Backtranseq, Transeq, Pepinfo, in addition to numerous extra tools not available elsewhere. Nonetheless, this list of resources can be useful to help navigate the oftentimes-daunting field of biological research.
Sharing insights is the impetus for scientific growth and success within the community. We encourage further discussion in the comments below. Feel free to leave a comment about any experiences you have had using any of the resources in this list as well as any other tools that might be helpful to other readers. We are working on compiling a comprehensive list of databases and repositories for molecular biologists which will be posted soon, so stay tuned. We look forward to hearing your thoughts!