Scientific visualization of DNA sequence matching in large-scale genomics sequencing

Abstract

OligoSpawn is a Linux-based software package for DNA pattern discovery. OligoSpawn can be used to discover two types of oligos (short DNA patterns of 20-50 bases long), namely unique and popular oligos, from large databases of gene sequences. The purpose of this project is to add a GUI for OligoSpawn, and then extend the OligoSpawn GUI to visualize the mapping of large numbers of short DNA reads from next-generation sequencing (NGS) to reference genomes. The GUI is being constructed in Python using PyPE as the IDE, wxpython as the GUI-building toolkit and Swig to wrap around the C and C++ based backend code. The report is segmented into three major sections: Overview of the software and concepts utilized; Techniques employed during implementation and the Final results.