Rationale:

To check the annotations of NapoleonB as a class in order to catch any mistakes that were made.

Procedure:

1. Using an already auto annotated version of NapoleonB on DNA Master gene 18 was confirmed to have the correct LORF.
2. Synteny was also updated for genes 19 and 20.
3. The rest of the genome was proofed as a class.

Results:

The synteny for genes 19 and 20 were updated using the phage KeaneyLin in addition to Nason. The rest of the genome was moderately corrected in order to fix entry errors.

Conclusions:

It can be confirmed that gene 18 was correct in its annotation. It can also now be concluded that genes 18, 19, and 20 do have synteny as shown in phamerator. It can also be concluded that the annotations for the phage NapoleonB are as of now correct.

Next Steps:

The next step will be to conduct an independent research project. We will also create a poster as a group in order to present at scholars week as a class, along with finalizing a class abstract.

Rationale:

To check the annotation of the phage NapoleonB and to edit/create an abstract for our assigned group.

Procedure:

1. Using an already auto annotated version of NapoleonB on DNA Master and the NapoleonB phage notes, gene 18 was checked to ensure the LORF was correct.
2. Using different elements from each of our own abstracts, a group abstract was compiled and submitted.

Results:

Gene 18 was verified as having the correct LORF. Our abstract included both Kathryn and Cooper’s abstracts as the basis for the structure, while elements of my material and methods and Lily’s introduction were also used.

Conclusions:

It can be concluded that the current annotation of gene 18 is correct and that our abstract matches up with the expectations set forth.

Next Steps:

The next step will be to continue working on a class abstract for our scholars week poster presentation and to begin working on our independent research project.

Rationale:

To annotate genes 18, 19, and 20 of the phage NapoleonB.

Procedures:

1. DNA Master was opened with the fasta file for NapoleonB being selected.
2. NapoleonB’s sequence was auto-annotated.
3. The ORF screen was opened and the RBS values were opened as well.
4. Gene 18 was then annotated.
5. Steps 2-4 were repeated for genes 19 and 20 respectively.

Results:

Gene 18:

Gene 19:

Gene 20:

Gene 18:

SSC:14865 – 16796, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with KeaneyLin gp NCBI BLAST q1:s1 0.99 0, Aligns with KeaneyLin gp18 PhagesDB BLAST q1:s1 0.99 0, Gap:95bp gap, LO:No, RBS:Kibbler7 and Karlin Medium 1.803 -5.081 No, F:minor tail protein, SIF-BLAST:Minor Tail Protein Supported by NCBI BLAST KeaneyLin gpNA AXH44156.1 0.99 0, Minor Tail Protein Supported by PhagesDB BLAST KeaneyLin gp18 0.99 0, GDSL-like Lipase/Acylhydrolase supported by a CD found from the pfam database gp pfam13472 NA 1.01E-11, , SIF-HHPred:NKF, SIF-Syn:minor tail protein, upstream gene is major tail protein, downstream gene is NKF, just like in phage Nason

Gene 19:

SSC:16816 – 17196, CP:Yes, SCS:BothGL, ST:SS, BLAST-Start:Aligns with KeaneyLin gp NCBI BLAST q1:s1 0.99 3E-86, Aligns with KeaneyLin gp19 PhagesDB BLAST q1:s1 0.98 6E-69, Gap:19bp gap, LO:Yes, RBS:Kibbler7 and Karlin Medium 2.381 -3.86 Yes, F:minor tail protein, SIF-BLAST:Minor Tail Protein Supported by NCBI BLAST KeaneyLin gpNA AXH44157.1 0.99 3E-86, Minor Tail Protein Supported by PhagesDB BLAST KeaneyLin gp19 0.98 6E-69, putative tail-component supported by a CD found from the pfam database gp pfam04883 NA 0.00924, , SIF-HHPred:NKF, SIF-Syn:NKF, upstream gene is minor tail protein, downstream gene is NKF, just like in phage Nason

Gene 20:

SSC:17193 – 21671, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arcadia gp NCBI BLAST q1:s1 0.99 0, Aligns with Nason gp22 PhagesDB BLAST q1:s1 0.99 0, Gap:4bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 2.535 -4.411 No, F:tape measure protein, SIF-BLAST:Tape Measure Protein Supported by NCBI BLAST Arcadia ASR79986.1 0.99 0, Tape Measure Protein Supported by PhagesDB BLAST Nason gp22 0.99 0, tape measure domain supported by a CD found from the TIGR database gp TIGR02675 NA 0.00000202, , SIF-HHPred:Phage-related tail protein supported by COG gpN/A COG5283 0.2708 1, SIF-Syn:NKF, upstream gene is NKF, downstream gene is NKF, just like in phage Nason

Conclusions:

It can be concluded that gene 18 codes for a minor tail protein as does gene 19. It can also be concluded that gene 20 codes for a tape measure protein. There were no significant challenges in annotating these genes.

Next Steps:

The next step will be to fix any errors found in the annotation of NapoleonB in order for it to be submitted to PhagesDB and subsequently NCBI.

Rationale:

To annotate gene 17 from the phage NapoleonB.

Procedure:

1. DNA Master was opened with the fasta file for NapoleonB being selected.
2. NapoleonB’s sequence was auto-annotated.
3. The ORF screen was opened and the RBS values were opened as well.
4. Gene 17 was then annotated.

Results:

Gene 17

SSC:12925 – 14769, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Tribby gp18 NCBI BLAST q1:s1 1 0, Aligns with Tribby gp18 PhagesDB BLAST q:s 0, Gap:1bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 2.486 -4.688 No, F:major tail protein, SIF-BLAST:Tail Protein Supported by NCBI BLAST Tribby gpNA ASR80469.1 1 0, Tail Protein Supported by PhagesDB BLAST Tribby gp18 100 0, , SIF-HHPred:NKF, SIF-Syn:major tail protein, upstream gene is NKF, downstream gene is minor tail protein, just like in phage Nason

Conclusions:

It can be concluded that gene 17 is a major tail protein, as well as identical to the major tail protein found in the phage Tribby.

Next Steps:

The next step will be to annotate genes 18-20 of the phage NapoleonB.

Rationale:

To input the annotation data for genes 48 and 49 into PhageNotes once proofed, and to proof the annotations of genes 30 and 31.

Procedures:

1. The document containing the annotations for gene 48 and 49 was opened.
2. A previously open DNA Master window with a already auto annotated version of Elesar was opened.
3. Proofed genes 48 and 49 with BLAST, HHPred, PhagesDB, and GeneMark and uploaded them into PhageNotes.
4. Proofed genes 30 and 31 with BLAST, HHPred, PhagesDB, and GeneMark.

Results:

Genes 48 and 49 were slightly altered to the correct state and put into PhageNotes. Genes 30 and 31 were found to be without fault.

Conclusions:

The annotations were uploaded to PhageNotes in order for proofing over our annotations to occur.

Next Steps:

The next step will be to continue practicing gene annotation in order to annotate the genome of the phage NapoleonB.

Rationale:

To fix the annotations of Elesar genes 48 and 49 and add SIF-BLAST and SIF-HHPred information.

Procedure:

1. Using a previously open and auto annotated copy Elesar on DNA Master genes 48 and 49 were viewed.
2. Fixed coding potential on gene 48 and added ran SIF-BLAST and SIF-HHPred for both.

Results:

Gene 48:

SSC: 34620, 35063 CP: yes SCS: Both BLAST-Start: Elesar, gp45, PhagesDB, Query 1 to Subject 1, 100%, 6e-83 Gap: 113bp gap LO: yes RBS: Kibler7, Karlin Medium, 2.611, -3.929, no SIF-BLAST: NKF SIF-HHPred: NKF

Gene 49:

SSC: 35215, 36054 CP: yes SCS: Both BLAST-Start: Nandita, NCBI, Query 1 to Subject 1, 95%, 8e-165 Gap: 151bp gap LO: yes RBS: Kibler7, Karlin Medium, 2.970, -3.344, yes SIF-BLAST: HTH DNA binding protein, NCBI, Nandita gp49, AYN58672.1, 82%, 8e-165 SIF-HHPred: Transcription factor MBF1 [Transcription], KOG, KOG3398, 98.31%, 5.6e-9

Conclusions:

Based upon the data gene 49 can be reliably called to be a gene that codes for Helix turn Helix DNA Binding Protein. For gene 48 however, there is no known function for its product as agreed to by the various data sources.

Next Steps:

The next step will be to continue practicing the annotation of genes and to familiarize myself with DNA Master with the future goal being the complete annotation of the phage NapoleonB’s genome.

Rationale:

To continue practicing genome annotation with DNA Master by annotating two genes of Elesar’s genome.

Procedures:

1. Used an already opened and auto-annotated copy of Elesars genome on DNA Master.
2. Annotated genes 48 and 49 of Elesar.

Results:

Gene 48: SSC: [34620, 35063], CP: yes, SCS: Both, BLAST-Start: Elesar, gp45, PhagesDB, Query 1 to Subject 1, 100%, 6e-83 Gap: 113bp gap, LO: yes, RBS: Kibler7, Karlin Medium, 2.611, -3.929, no

Gene 49: SSC: [35215, 36054], CP:yes, SCS: Both, BLAST-Start: Nandita, NCBI, Query 1 to Subject 1, 95%, 8e-165, Gap: 151bp gap, LO: yes, RBS: Kibler7, Karlin Medium, 2.970, -3.344, yes

Conclusions:

From the results gathered it can be concluded that I learned more about how to annotate genomes on DNA Master.

Next Steps:

The next step will be to continue practicing with DNA Master in annotating Elesar’s genome in order to eventually annotate the genome of the phage NapoleonB.

Rationale:

To continue practice annotation of Elesar by becoming more familiar with how to BLAST.

Procedure:

1. Using an already open and auto-annotated Elesar Mastering DNA window, a BLAST search of gene 1 was conducted using the in program BLAST search feature.
2. A BLAST protein search for gene 1’s protein sequence was also conducted using the NCBI BLAST program.
3. Step 2 was repeated for the PhagesDB BLAST program.
4. Analyzed Results.

Results:

For both NCBI and the DNA Master BLAST searches, all hits had scores less than 40. For the Phages DB BLAST there was a hit with a score of 178 and an E value of 2e-45, with the hit being the Elesar gene 1 unknown protein.

Conclusions:

Based upon the results it can be concluded that the protein for gene 1 is unknown as shown by the BLAST result from Phages DB, considering that both the sequence blasted and the hit were actually the same genes from Elesar.

Next Steps:

I will continue practicing genome annotation via DNA Master using the phage Elesar’s genome in order to eventually annotate the genome of the phage Napoleon B.

Rationale:

To learn how to BLAST genomes and further gain understanding of DNA Master using the genome of the phage Elesar.

Procedure:

1. Opened Elesar and adjusted local settings by inserting“SSC: CP: SCS: ST: BLAST-Start: Gap: LO: RBS: F: SIF-BLAST: SIF-HHPred: SIF-Syn”.
2. Autoannotated Elesar
3. Opened ORFs for Elesar and viewed them

Results:

A greater understanding of DNA Master, specifically auto-annotation and ORFs,  was achieved through practicing with Elesar.

Conclusion:

My understanding of DNA Master was strengthened, which will be useful for further practice annotation on Elesar and the future annotation of NapoleonB’s genome.

Future Plans:

To continue to learn how to use DNA Master in order to annotate the genome of the phage Napoleon B and publish the annotations on PhageDB.