02/19/17

Kiersten Scott

The purpose of this lab was to identify and address any areas of concern on the annotations of the Lore genes 14 and 15.

Method

The method of this lab builds on the method from the last three labs.  By using the Glimmer, GeneMark, PhageDB, NCBI, HHPred, Phamerator, and Starterator programs I was able to lead a  fellow student through the process of annotating a gene.

Methods

First, we opened the lore genome in Glimmer GeneMark, and Phamerator to assess coding potential and whether the three programs agreed with the chosen start site. Then using the Pham numbers we ran the genes to Starterator. After we felt that we had collected enough evidence we selected a start site and checked its Shine Delgarno reading to see if our start site was acceptable or if a better option existed. Once we were satisfied with the results we recorded the start site, the gap or overlap, and whether the gene had the longest open reading frame. The next step was to identify any possible function so we ran the protein products of the genes through NCBI, PhagesDB, and HHPred and recorded the best possible hits.

Results

Both of us were able to successfully annotate a gene as well as address a region of uncertainty with the start site of gene 15. After reviewing our evidence we decided to use a gene with a shorter open reading frame with aligned best with the calls from Starterator our BLASTs and the Shine Delgarno score.