SEA-PHAGES | Annotation check questions

Link to this post \| posted 03 May, 2018 18:46
Tamarah_Adair	Hi. We have had our annotations returned because we did not realize there was a new annotation guide (sorry!) Would you mind looking at these examples annotations and answer a few questions before we upload our DNAMAster files. 1. We are annotating A. globiformis phages. There are not many annotated phages or known gene functions in these clusters, so starterator is Not Informative, correct? 2. Synteny is described in detail, but for phages in new clusters, which phage should be referenced, or should we just use the list order and not reference the genome? or say NKF? For example, terminase below? SSC: start: 1349bp, stop: 1984bp CP: Yes SCS: both ST: NI Blast-Start: Arthrobacter sp. TMN-18, gp: N/A NCBI, Q:25S:27 coverage: 0.92 E-value: 0 , Nandita_Draft, gp: 5 PhagesDB, Q:1S:1 coverage: n/a E-value: e-107 Gap: 4bp Overlap LO: NA, RBS: Kibbler7, Karlin Medium, Zscore: 2.23, Final Score: -4.085, No F: terminase, small subunit SIF-Blast: NKF SIF-HHPred: Phage terminase, small subunit [Mobilome: prophages, transposons]COGN/a gp: N/a accession number: COG3747 alignment: 0.132 probability: 99.65 SIF-Syn: NKF Notes: NCBI hit is bacterial/hypothetical, Nandita is a draft, so the only hit is a HHPRED hit to COG. 3. Is it a correct interpretation of the guide to put NKF for all SIF if the gene function is determined to be NKF, or do you want to see the hits that were used to come to that conclusion. For example, is this annotation acceptable for a gene of nkf? SSC: start: 8565bp, stop: 8840bp CP: Yes SCS: both ST: NI Blast-Start: Arthrobacter sp. EpRS71, gp: N/A NCBI, Q:3S:4 coverage: 96 E-value: 8.6E-38 , Nandita_Draft, gp: 14 PhagesDB, Q:1S:12 coverage: N/A E-value: 2E-30 Gap: 4bp Overlap LO: NA, Lorf had a 39 bp overlap with the previous gene RBS: Kibbler7, Karlin Medium, Zscore: 1.137, Final Score: -7.054, No F: NKF SIF-Blast: NKF SIF-HHPred: NKF SIF-Syn: NKF Notes: 4. How do we add an underscore in the locus tag for all the genes at once? Thank you!

Link to this post | posted 03 May, 2018 18:46

Hi. We have had our annotations returned because we did not realize there was a new annotation guide (sorry!) Would you mind looking at these examples annotations and answer a few questions before we upload our DNAMAster files.
1. We are annotating A. globiformis phages. There are not many annotated phages or known gene functions in these clusters, so starterator is Not Informative, correct?
2. Synteny is described in detail, but for phages in new clusters, which phage should be referenced, or should we just use the list order and not reference the genome? or say NKF?
For example, terminase below?

SSC: start: 1349bp, stop: 1984bp CP: Yes SCS: both ST: NI Blast-Start: Arthrobacter sp. TMN-18, gp: N/A NCBI, Q:25S:27 coverage: 0.92 E-value: 0 , Nandita_Draft, gp: 5 PhagesDB, Q:1S:1 coverage: n/a E-value: e-107 Gap: 4bp Overlap LO: NA, RBS: Kibbler7, Karlin Medium, Zscore: 2.23, Final Score: -4.085, No F: terminase, small subunit SIF-Blast: NKF SIF-HHPred: Phage terminase, small subunit [Mobilome: prophages, transposons]COGN/a gp: N/a accession number: COG3747 alignment: 0.132 probability: 99.65 SIF-Syn: NKF Notes: NCBI hit is bacterial/hypothetical, Nandita is a draft, so the only hit is a HHPRED hit to COG.
3. Is it a correct interpretation of the guide to put NKF for all SIF if the gene function is determined to be NKF, or do you want to see the hits that were used to come to that conclusion. For example, is this annotation acceptable for a gene of nkf?

SSC: start: 8565bp, stop: 8840bp CP: Yes SCS: both ST: NI Blast-Start: Arthrobacter sp. EpRS71, gp: N/A NCBI, Q:3S:4 coverage: 96 E-value: 8.6E-38 , Nandita_Draft, gp: 14 PhagesDB, Q:1S:12 coverage: N/A E-value: 2E-30 Gap: 4bp Overlap LO: NA, Lorf had a 39 bp overlap with the previous gene RBS: Kibbler7, Karlin Medium, Zscore: 1.137, Final Score: -7.054, No F: NKF SIF-Blast: NKF SIF-HHPred: NKF SIF-Syn: NKF Notes:

4. How do we add an underscore in the locus tag for all the genes at once?

Thank you!

Link to this post \| posted 03 May, 2018 20:05
welkin	Hi Tammy. 1. STarterator is informative if there is more than one other pham members. It doesn't matter if the phams have a known function or if the genomes still have draft annotations. The point is to see if the starts are conserved throughout the group. 2.for the synteny note, you should be looking at the gene content of your own genome. Does the terminase fall in the left arm of the genome and is it followed by the portal? Finding other genomes to reference can be helpful but is not essential. 3. you don't need to list all the hits but it would be good to indicate that all the analyses were run. 4. you check the box labeled "override" that is to the right of the locus tag box in the validation tab. Thanks! Welkin

Link to this post | posted 03 May, 2018 20:05

welkin

Hi Tammy.

1. STarterator is informative if there is more than one other pham members. It doesn't matter if the phams have a known function or if the genomes still have draft annotations. The point is to see if the starts are conserved throughout the group.

2.for the synteny note, you should be looking at the gene content of your own genome. Does the terminase fall in the left arm of the genome and is it followed by the portal? Finding other genomes to reference can be helpful but is not essential.

3. you don't need to list all the hits but it would be good to indicate that all the analyses were run.

4. you check the box labeled "override" that is to the right of the locus tag box in the validation tab.

Thanks!
Welkin

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