February 22

Lab 6: Lore_Draft Annotation

Jess Hastings

Date of Work: 2/14/2017

Rationale: The purpose of the lab was to check annotations of the Lore_Draft gene that was annotated during lab five. Additionally, genes that were annotated by other groups, but overlapped into our region were annotated and checked against the other group’s for differences. After all genes in the region were annotated, each group put together a PowerPoint presentation will annotation details and proof to present to the class.

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

Methods:

Run an Auto-Annotation of Lore_Draft in DNAMaster
For each gene in the region, check and, if needed, change the following parts of the annotation:
- SSC: call start of the gene
- CP: coding potential found on GeneMark (on phagesdb)
- SD: score, if it is the best score and if not why, z-score
- SCS: does it agree with Glimmer and GeneMark
- Gap: calculated from start/stop location
- NCBI Blast: protein product on NCBI
- Phagesbd BLAST: protein product on Phagesbd
- HHPred: best hit with e value or no good hit
- LO: longest open reading frame
- ST: does it agree with Starterator
- F: function
- FS: evidence that supports function decision
Fill each part of the annotation into the Lore_Draft Google document
Change status on the home page to completed
Create a PowerPoint to share annotations and evidence for decisions made with class

Conclusions:

Our region of the Lore_Draft genome was bp 1401-2800 which contained genes 4-6. Kayla and I decided to each annotate one gene and gene 6 was annotated by group 3. I annotated gene 5 in our region.

Figure 1: Region of Annotation for Group 1

The following annotation is my results for gene 5:

Start: 2294bp Stop: 2497bp FWD GAP: 5bp Gap SD Final Value: SD Score: -3.122 (Best score) Z-Value: 2.909 CP: The gene is covered SCS: Agrees with Glimmer, Agrees with GeneMark NCBI BLAST: hypothetical protien [Arthrobacter phage Jessica] q:1 s:1 E-Value: 3e-34 CDD: No good hit PhagesDB BLAST: Function Unknown [TymAbreu 5] E-Value: 1e-27 HHPred: No good hit LO: Yes ST: Agrees with Starterator F: NKF FS: NCBI, PhagesBD, HHpred Notes:

Gene 5, was a pretty simple gene to annotate. There was not start changes that needed to be made because the call that was made in the auto annotation agreed with Starterator, the GeneMark coding potential, and produced a q:1:s:1 score on the NCBI Blast. However, there was no function found for gene 5. The Blast did not return any conserved domain hits and additionally HHPred did not have any good hits. So, gene 5 was labeled as “No Function Known”.

Evidence for these calls can be seen in the follow figures:

Figure 2: Coding Potential of Gene 5 from GeneMark

Figure 3: NCBI Blast results for Gene 5

Figure 4: Phagesbd Blast results for Gene 5

Figure 5: HHPred results for Gene 5; no good hit

I also annotated Gene 6, to double check Group 3. I agreed with all of their annotations which came from the auto-annotation done by DNAMaster. There were no changes made to gene 6. The follow annotation is the result:

Start: 2549bp Stop: 3709bp FWD GAP: 51bp Gap SD Final Value: SD Score: -4.629 (5th best score) All the others don’t cover all coding potential. Some are under 200 base pairs long. Z-Value: 2.16 CP: The gene is covered SCS: Agrees with Glimmer, Agrees with GeneMark NCBI BLAST: portal protein [Arthrobactor phage Decurro] q:1 s:1 E-Value: 0.0 CDD: pfam04860 E-Value: 1.89e-19 PhagesDB BLAST: Portal Protein [Yank_6] E-Value: 0.0 HHPred: 3kdr_A, HK97, family phage portal protein E-Value: 7.1e-42 LO: Yes ST: Agrees with Starterator F: portal protein FS: PhagesDB, NCBI, HHpred Notes:

Gene 6 is a phage portal protein. This is decided upon because of the Blast results as well as the CDD information gathered. Additionally, HHPred confirmed the results that it was a portal protein.

Evidence for Gene 6: