We found that the annotated boundaries for control elements in commercial plasmids were inconsistent and sometimes clearly wrong. Identifying plasmid control elementsĬoding sequence features are relatively straightforward to define, but for control elements such as promoters and transcription terminators, the boundaries are less obvious. With the increasing popularity of gene synthesis, many researchers now use codon-optimized versions of common coding sequence features, so our detection system was enhanced to allow searches for a perfect protein sequence match even when the DNA sequence has changed. For a coding sequence feature that may be used to make fusion genes, detection needs to occur even if one or two codons are missing at the beginning or end of the feature. Empirical tests indicated that a reasonable rule is to require at least 96% sequence identity when detecting a reference feature. Instead, we identified common variants, and then crafted a detection algorithm that tolerates occasional mismatches or indels. It proved to be impractical to catalog every variant of a feature. These plasmids contain features such as antibiotic resistance markers and replication origins, but there is extensive heterogeneity in the feature sequences due to genetic drift and the use of genes from different microbial strains. The source of common features was our collection of popular plasmid sequences. Development of this tool required creating a database of common features, and devising rules for identifying a feature even when the match is imperfect. This algorithm enables one of SnapGene’s most popular aspects - its ability to annotate a raw plasmid sequence and display frequently used genes and control elements.
N GENE SEQUENCE SNAPGENE VIEWER SOFTWARE
Development of software with these qualities is an ongoing process that involves iterative refinements in response to customer feedback.Īn example of this approach is SnapGene’s algorithm for detecting common features. SnapGene has been engineered to be easy and enjoyable to use. Instead of crowding the interface with every possible option, we place the most important controls front and center, and make specialized controls available when needed. For every task, we envision what the user wants to do and make the path to accomplishing their goals as intuitive and painless as possible. But what makes software good? Fortunately, that question has been thoroughly answered by experts in human-computer interaction (HCI), and we have adhered rigorously to HCI principles. SnapGene was created to alleviate these problems through good software design. In the 21st century, many molecular biologists didn’t know the complete sequences or properties of the DNA molecules they were using. Records of plasmid construction were often incomplete or nonexistent. Primer design was done painstakingly by hand. Preventable errors in the design of cloning strategies set experiments back days or even weeks.
![n gene sequence snapgene viewer n gene sequence snapgene viewer](https://www.snapgene.com/plasmids/generated/basic_cloning_vectors/pUC19L/pUC19L.png)
While there were software tools available to biomedical researchers manipulating DNA sequences on a daily basis, many found these tools inadequate for planning, visualizing, and documenting their procedures. This post was contribued by guest bloggers Aline and Benjamin Glick from SnapGene.