Jess Hastings

Date of Work: 1/31/2017

Rationale: The purpose of this lab was to learn the Phamerator software. This software contains all phages that have been recorded, and creates maps that can compare the similarities of genes.

Tools Used: DNAMaster, DNAMaster Quick Start Guide, NCBI Website, Phagesdb Website, Phamerator

Methods: 

Annotation Continued:

1. To perform a Blast:
   1. Select the gene you would like to BLAST
   2. Select Product and copy the chain of amino acids listed
   3. Go to the NCBI website or phagesbd.org (wherever you would like to perform the blast)
   4. Select Protein Blast
   5. Paste the amino acid chain into the query box
   6. Select BLAST
   7. The Blast may take a little while to run, but after it is complete you can analyze the matches and note the error factor to determine accuracy
2. After performing a blast on NCBI and phagesbd list the closest result, score, and evalue under the BLAST note
3. Compare NCBI and phagesbd results to determine the function of the gene that is being annotated, record function under the F: note
4. Under the FS: note, write reasoning for why that function was selected, reference phagesbd and NCBI results

Phamerator:

1. Enter virtual box, open Phamerator and search the phage Link
2. Select the phage Link along with 2 other similar phages
3. Click “Map” in the upper left hand corner to compare the genomes of these phages

Conclusions: This lab was helpful because Phamerator provides a strong visual to be able to compare phage genomes. Also, a full manual annotation was done on Link Gene 22, using all the technology that we have learn at this point. My annotation results were:

Link Gene 12

Annotation:

Original Glimmer call @bp 6820 has strength 13.98
SSC: 6853-7170 Forward CP: Covers All SD: -5.552 but not best score, -1.414 is more practical SCS: Glimmer called at 6820, GeneMark called at 6853 Gap: 6bp gap
BLAST:
On phagesbd: Toulouse_11, function unknown, 116, score: 232, error: 8e-62
On NCBI: Hypothetical Protein, score: 237, error: 3e-79
LO: 318bp ST:n/a F:Hypothetical Protein FS: BLAST evalue on NCBI, top 15 all same results, 100% match