Date of Lab: 01/31/17

Rationale: The purpose of the lab was to practice genome annotation and learn how to use Phamerator.

Tools used: DNA master, NCBI, Phamerator

Procedures:

1. Open the software Phamerator through virtual box and login with the password “phamerator”.
2. Under “Phages” tab> search the interested gene (It will allow you to look at multiply genes at the same time) > MAP
   1. the number in the colored box = gene number
   2. number above the box = pham number
   3. number in (#) = number of members in that pham
   4. lines on the graph: identifying sequence that are similar on other part/ duplication/different place/ phage
   5. upper gene= forward
   6. lower gene = reverse
3. If we pointed at the gene/the rectangle, it would show the function of the gene(only apply on some genes)
4. Annotate the assigned gene (gene 22)

Conclusion:

We got to learn to use a new tool to help us to annotate the genes with more details and have more practice on annotating the genes.

Notes:

• each ruler = genome
• rectangle = auto annotated gene
• high gene density
  • shouldn’t have too many gap/overlap–should be packed
• there will be gap for promoter between genes
• If it is a perfect match :
  • query coverage ~200%
  • E value ~ 0
• Long DNA = tap measure gene
• Short gene = regulator
• F = function
• Fs = function source: blast, pharmarater, HHpred, cdd(conserved domine), record best blast

Theresa WangChin Wong

Date of Lab: 02/21/17

Rationale: The purpose of this lab was to present the annotation of our assigned and to ensure the annotation was accurate.

Procedures:

1. Add the Q:S value to the google spreadsheet.
2. Help reannotate the genes of other groups if necessary.

Notes:

*only shorten a gene If there’s too much overlap
*Enter new start site into DNA Master: input the new start site > hit the calculator button > “Post”

*When we are deciding the start site, we prefer to choose the gene with a better SD score than with the longer ORF.

Conclusion:

I learned a lot from learning about how the other gene area annotated and why changes were made on annotating the genes base on different situation.

Theresa WangChin Wong

Date of Lab: 02/14/17

Rationale: The purpose of this lab was to annotate Lore for the assigned gene and put the results on the excel spreadsheet.

Tools used: DNA master, NCBI, Phamerator, Starterator, Glimmer, GeneMark

Procedures:

• We did not make any changes on gene 13.
• Start: 7279bp Stop: 9276bp FWD GAP: 110bp Gap SD Final Value: SD Score: -4.389 (2nd best score) Z-Value: 2.209 CP: The gene is covered SCS: Agrees with Glimmer, Agrees with GeneMark NCBI BLAST: Tapemeasure protein Arthrobacterphage Toulouse E-Value: 0.0 CDD: Phage-related protein [Mobilome: prophages, transposons] E-Value: 5.90e-11 PhagesDB BLAST: StewieGriff_Draft_13, function unknown, 665 Q:1 S:1 E-Value: 0 HHPred: No good hit LO: Yes ST: Agrees with Starterator F: tape measure protein FS: Phages DB, NCBI, HHPred, Phamerator

• We chose the #1 gene with the 2^nd best score and the longest ORF to be our starting site. Since it also agrees with Glimmer, GeneMark and Starterator, and it cover most of the gene. We did not choose the gene with the best score(gene9) because it would create a larger gap.

• Gene #1 has the most number of blue vertical bars on Starterator and that’s the gene Starterator suggested.

We got a 0.0 E value on NCBI BLAST, its function is tapemeasure protein

• We got Query1: Subject 1 on NCBI BLAST, that’s mean our query gene match with the subject(top hit) gene with the same length. So we can agree with the start codon.

• Phagesdb: StewieGriff_Draft_13, function unknown, 665 has an e value of 0.0.
• Conserved domains
• NO hit on HHPred

Conclusion:

With the help of the excel spreadsheet, we did the annotation step by step and we are able to compare our results with other genes at the same time.

Theresa WangChin Wong

Date of Lab: 02/07/17

Rationale: The purpose of the lab was to annotate our assigned genes (ranging from 8401-9800) and learn how to use Starterator.

Tools used: DNA master, NCBI, Phamerator, Starterator, Glimmer, GeneMark

Procedures:

1. Download the Fasta file for Lore on fastdb website and load it into DNA master.
2. To figure out which gene we should annotate, we compare our assigned range with the 5’End & 3’End ranges (on the Features tab). And we found out we it mostly cover gene 13 and overlap with gene 14.
3. Fill in the start coordinate, stop coordinate, FWD/BKWD, Gap/Overlap
4. Coding potential :if the gene (black horizontal bar) is longer than the line graph, it is covered
5. Shine Delgarno :SD score & Z-Value
6. start choice source: does it agree with Glimmer & GeneMark?)
7. LO: longest ORF value
8. NCBI: blast it on NCBI, record the name of the best hit and its E-Value
9. Conserved Domains: Click the button above the line graph on the NCBI website. Record the best hit & its E-Value.

• Blast on Phages DB & HHPred
• Starterator: Open Virtue Box>Starterator>

”Choose what you want to Starterate” :Pham

“Pham Number”: 6177 find it on the Phamerator (the number on top of our assigned gene)

>Link to Report > see whether it agree with Starterator

start choice: base on the gene with the most blue vertical bar (other vertical bar with color than blue = random)

• Function: find it through Phamerator
• Function source: Phages DB, NCBI, HHPred, Phamerator

Conclusion:

I became more familiar with the whole process of annotating the gene, with a organized google spreadsheet. And the picture below is the result of my  annotation.