Purpose: The purpose of this lab was to learn how to do a BLAST on NCBI and PhagedDB, and to learn how to annotate a gene.

Tools/Procedures: 

Tools:

• DNA Master
• NCBI and PhagesDB
• GeneMark
• Annotation Guide

Procedures:

1. A BLAST was performed on Elesar gene 1 with NCBI and PhagesDB.
2. The start was found to be at bp 45, making the coordinates of the gene 45, 353.
3. The Coding Potential (CP) was found to include all coding potential identified by GeneMark.
4. The start choices predicted by Glimmer and GeneMark were the same, but neither was used.
5. The BLAST results found no significant alignments for Elesar 1.
6. The annotation was saved.

Results:

The BLAST results yielded no significant alignments for Elesar 1. The annotation was started but was not completed.

Conclusions:
Because the E value for Elesar gene 1 was so high, ranging from 3.4 to 10, it was concluded that there was no significant alignment found. Both NCBI and PhagesDB did not have a gene that significantly matched Elesar gene 1. The annotations for this gene were begun, but not finished. The start of the gene was moved to the longest open reading frame, which also included all of the coding potential identified in GeneMark. While the start codon was TTG and this is rare, it is possible, and this start was identified as an overall better fit.

Future Work: 
Future work will include finishing the annotation of Elesar gene 1, and then proceeding to BLAST more of Elesar’s genes. Further practice will be done with Elesar to later annotate NapoleonB.