Multi gene analysis tool for Virus Induced Gene Silencing

Project Summary

Virus Induced Gene Silencing (VIGS) is a very useful method of studying gene function in plants.  For this method to be effectively employed, the target gene fragment introduced into the virus vector has to have a specific sequence.  Identifying that specific sequence will allow for the silencing of target genes while influencing as few off target genes as possible. To aide in this effort, Sol Genomics Network (SGN) created the SGN VIGS Tool to help researchers design VIGS constructs with a user-friendly and highly customizable web tool. The original version of the tool only worked with one sequence at a time, yet researchers could require the silencing of hundreds of genes to study particular gene functions in large screening experiments.  With this in mind, a new algorithm was developed to improve the tool to accept multiple sequences at a time. Implementation of the algorithm was done on a Stand Alone version of the SGN VIGS Tool, incorporating several programming languages and software. The result of this algorithm is a new feature on the SGN VIGS Tool, Bulk, that will accept a file of multiple Fasta sequences, and return the appropriate construct sequences, and target and off target gene information. The user also has the option to upload expression data that can accompany the results of their target and off target gene information. Future improvements will involve the addition of primer3 to further aide researchers in making multi gene virus constructs more efficiently.

My Experience

In creating the VIGS Tool Bulk, I was exposed to new programming languages and software such as Perl, Catalyst, and the Command-line interface. Often  my code would return errors or I would encounter new processes, and need  to do in depth research online to fix the issue.  Consequently my knowledge and proficiency in those languages and software have increased significantly.  I now also have extensive experience with web tool development. The members of the Mueller lab were great resources all summer, especially my mentor, Noe Fernandez. With his guidance, I was able to gain a greater understanding of the relationship between biology and computer science, and how to code more efficiently—something that will be invaluable if I pursue a career in bioinformatics.