Automate the process of analyzing and comparing DNA and protein sequences.
This project of mine is intended on creating a more efficient way of analyzing cDNA sequences as part of the Waksman Student Scholars Program (https://www.waksman.rutgers.edu/news). Over the course of many years, Rutgers has been studying Landoltia punctata (duckweed) and its potential for biofuel and bioremediation. The university generates many cDNA sequences (strands derived from mRNA in duckweed) and provides them to students for analysis.
This study has been going on for quite a long time and is involving a large number of high schoolers. Many of the professors managing the WSSP have to ensure that students correctly analyze their sequences to the fullest extent, and this can take away valuable time. While students are still able to be exposed to research, further progress into the study has only been hampered.
My project intends to increase the efficiency of analysis of clones while ensuring students are able to pursue a research-related activity. Rather than wait for weeks after a submission for a professor's response, students can use the project to check their work before submission, and professors and faculty may also use this for their respective analyses.
As of April 2019, BLASTn, BLASTx, and BLASTp methods may be invocated given a certain sequence to be analyzed. The scripts I have created will place all data and necessary output into a .xls file (excel) workbook.
Please note that creating these scripts has taken quite a long time for me! Scouring through the scarce API documentation on NCBI and unfamiliar python packages is a time-consuming task. Consequently, there are still many more parts that are not yet (but I would like in the future) included. The scripts do complete a majority of the analyses, but work can still be done. Feel free to create any commits to this repository for any of you involved in WSSP!
Please also note that I and any contributors are not responsible for any academic integrity violations. We implore that individuals looking for help in their analyses put their best personal effort into them before consulting project resources.