Annotation of Microbacterium Phage Stagni through DNA Master

Swasey, Royce, Tamia Waller, Joshua Thomson, and Jacob Kagey

This semester, our Bioinformatics class annotated the DNA Sequences belonging to two of our previously isolated bacteriophages, Stagni and Kady. It can be difficult to completely understand our process if it is not yet understood what exactly it means to “annotate” a gene. Gene annotation involves describing different fragments of a DNA sequence with the hopes of revealing which sections of that sequence is actually in fact a gene. In short, annotation ultimately reveals a DNA sequence’s entire genome arrangement. Our annotation procedure required us to identify where exactly individual genes were located and additionally required us to determine all of the coding areas on those genes. There are many different approaches that could be taken to do the following.  Our process, however, included prediction based methods (which allowed us to find genes/gene structures based on nucleotide sequence) and sequence similarity methods (which allowed us to align our DNA with other sequences and proteins from different or similar species for comparison). We used a combination of software informers to do the following, including the freeware DNA sequence editor DNA Master and the computer program Phamerator. Synchronized use of the two programs allowed us to break down our phage’s DNA sequence into various components and generate genome maps that incorporated nucleotide and amino acid sequence relationships. As a result, we were able to assort our protein-coding genes into “phamilies” of related sequences using comparisons to generate a database of gene relationships.