With the advent of the electronic lab notebook era, based on the standardized cross-team workflow, molecular biologists and chemists are able to promote the research and development of new drugs in a more synergistic and efficient way. However, in the field of biology industrial software, China is still in its infancy and currently relies mainly on foreign imports. Relying on foreign software has some potential drawbacks, mainly in terms of data security and R&D costs.
Data security: Using foreign software usually means that the user’s data will be sent to foreign servers, which may be intercepted during transmission or accessed by unauthorized third parties on the servers. This poses a very serious risk for data that contains sensitive information, such as patient genetic data and new drug development data. In addition, this can also lead to legal issues, as many countries and regions have strict regulations on data export.
R&D Costs: Foreign software usually charges higher fees, especially for some specialized biology research software. This constitutes a considerable burden for research institutions and enterprises, especially those with relatively tight funds. In addition to the direct purchase costs, foreign software may also bring some implied costs. For example, due to differences in the language and cultural background in which the software is used, users may need to invest extra time and effort to learn and familiarize themselves with its use. In addition, obtaining technical support may also become more difficult due to differences in time zones and languages.
Some researchers have tried to use dozens of open source software to transfer data, however, this method is complicated to operate, cannot guarantee data security, and the results are often unsatisfactory, wasting a lot of valuable time.
In order to meet the above challenges, Trunetech proposes a solution: iLabPower Sequence Editor. iLabPower Sequence Editor is an important part of iLabPower R&D management platform, which allows biologists to no longer be constrained by foreign software, and no longer need to put their data in foreign countries. It is equipped with visual sequence editing function, and at the same time, the design process can be recorded in the experimental record book.
Figure 1 | iLabPower Sequence Editor: a homegrown biological sequence design tool integrated in the electronic lab notebook.
iLabPower Sequence Editor supports the completion of the upstream and downstream processes from sequence creation, sequence editing to sequence validation in one go on the same platform. Taking plasmid construction, a common molecular biology experiment, as an example, the key steps in the classic process, including selecting target genes and vectors, designing primers for PCR amplification of target fragments, selecting appropriate endonuclease for pre-assembly cutting, and checking the product by sequencing results, can all be completed in iLabPower Sequence Editor. The multiple work steps are centralized in one platform, which guarantees the traceability and reproducibility of the data. The recent popularity of CRISPR and cyclic RNA construction have a similar sequence design process as plasmid construction, which is also a potential application scenario for iLabPower Sequence Editor.
Figure 2 | iLabPower Sequence Editor The Sequence Editor supports the top-to-bottom sequence design process from sequence creation, to sequence editing, to sequence verification.
Check out the details of iLabPower Sequence Editor 1.2, which will be released soon!
Create Sequences
The iLabPower Sequence Editor supports creating sequences in a variety of ways:
- Importing fasta sequence files
- Import a fasta sequence file, import a genbank or other annotated sequence file.
- Import a fasta sequence file Import a sequence file with annotations such as genbank
iLabPower Sequence Editor supports users to customize the labeling classification of each sequence in the electronic lab notebook, which can be adapted to the actual development scenario of each team for sequence management and searching. The design and modification process of each sequence is fully recorded in the electronic lab notebook, which realizes the fine control of data history in teamwork and guarantees the reproducibility of the experimental results.
After the sequence is imported, iLabPower Sequence Editor can automate the sequence processing, including generating sequence coordinates, switching sequence case, copying/replacing/inserting/deleting specified parts of the sequence, and searching and locating the sequence. In the editor, DNA sequences can be copied in various formats, including forward and reverse strand, or forward and reverse strand of corresponding RNA and protein sequences, which no longer requires users to calculate manually, avoiding manual errors in the basic and tedious process, and saving a lot of time that can be invested in meaningful data interpretation and design.
The common sequence analysis process starts from obtaining gene and vector sequences, usually the result of downloading or sequencing is a single-stranded sequence, which can be imported into iLabPower Sequence Editor to automatically generate complementary strands and construct double-stranded DNA sequences to support the subsequent design work.
The iLabPower Sequence Editor not only supports displaying and editing at the precision of specific base sequences, but also displays the sequence as a whole in the form of linear or circular maps. On the map, annotations, primers, digestion sites and other information can be displayed in a personalized way, which is convenient for the construction and design of plasmids, CRISPR, miRNA and other structures.
Figure 3 | iLabPower Sequence Editor creates, manages and visualizes sequences.
Nucleic acid sequence analysis
- DNA property calculation and primer design
iLabPower Sequence Editor automatically calculates basic DNA properties, including annealing temperature, GC content, and sequence length, etc., which is very convenient for primer design. iLabPower Sequence Editor also provides an automatic primer design function based on Primer3, which automatically generates pairs of primers or single primers under the sequence range and primer parameters specified by the user and displays primer property parameters for comparison and selection. The primer parameters are displayed for comparison and selection.
Figure 4 | Primer design with iLabPower Sequence Editor
- Enzymatic site display
In the construction of various vectors, the use of restriction endonucleases is the basic step of sequence shearing. iLabPower Sequence Editor automatically identifies the enzyme cleavage sites in the sequence based on the NEB-Enzyme Finder database and displays them on the sequence and map. You can also search for specific enzyme sites in the editor to speed up the design of sequence cuts and substitutions.
Figure 5 | Browsing and searching for cleavage sites with the iLabPower Sequence Editor.
- Open Reading Frame Recognition
In the process of gene expression, the existence of open reading frames is one of the main mechanisms that cause the diversity of gene expression, and the diversity of expression products has a significant impact on the quality control in the development of new drugs. iLabPower Sequence Editor can automatically identify the open reading frames, support the identification of multiple start codons, support the user to customize the minimum length of the translation product, and provide an intuitive visual display of the open reading frames. Figure 6 | Using iLabPower Sequence Editor
Figure 6 | ORF-based diverse expression analysis using iLabPower Sequence Editor
Amino acid sequence analysis
- Protein biochemical characterization
For translatable DNA sequences, iLabPower Sequence Editor can automatically translate them into amino acid sequences corresponding to codons, and support users to select amino acid sequence coordinates and color schemes.
For the generated amino acid sequences, iLabPower Sequence Editor can automatically analyze the amino acid components of proteins, list the percentage of each amino acid, and study the properties of proteins by protein composition analysis. In addition, it is also possible to categorize the amino acids according to their hydrophilic and hydrophobic properties, and find those hydrophobic groups that may be transmembrane regions. In turn, parameters such as isoelectric point, molecular weight, extinction coefficient, instability, etc. of proteins can also be analyzed to study protein properties in general.
- Antibody Design
Antibody drugs are currently a popular research area for new drugs. iLabPower Sequence Editor can automatically identify the CDR region in the sequence, i.e. the highly variable region that plays a key role in antigen recognition, which facilitates antibody design.
Figure 7 | iLabPower Sequence Editor shows protein biochemistry and CDR region.
Comparative Analysis
- BLAST
Blast analysis is a cornerstone of bioinformatics analysis, which has been widely used in basic evolutionary and developmental research, as well as clinical molecular diagnostics and design of new biological drugs. iLabPower Sequence Editor supports one-click jumping, automatically submits the target sequence fragments as query in NCBI-blastn page, and predicts the query sequence by comparing with NCBI database. Possible functions.
- Dual Sequence Alignment
iLabPower Sequence Editor supports dual sequence alignment of DNA and amino acid sequences to find the affinity between the two sequences. The comparison algorithm and parameters can be adjusted individually, and the comparison results can be visualized to show the conserved homologous regions and highly variable regions at a glance.
Figure 8 | iLabPower Sequence Editor Dual Sequence Comparison Results
New biopharmaceuticals have demonstrated unparalleled effectiveness and potential in the treatment of once-unsolved diseases, such as cancer and genetic diseases. iLabPower Sequence Editor, with its high efficiency, ease-of-use, and safety design concepts, has undoubtedly brought a new path for innovative research in laboratories and biopharmaceutical companies. It realizes that sequence design work can be done in one go, from upstream design to downstream testing, on a platform with highly controllable data security and reproducibility!
In addition, based on the in-depth understanding of the needs and pain points in the field of bio-new drug R&D, NeoTrident is also constantly upgrading the interaction and convenience of the software, enriching the bioinformatics functions provided by the software, and is committed to escorting the intellectual property rights and rapid research and development of China’s bio-innovative drugs!
