SEA-PHAGES | Annotations of Microbacterium foliorum

Link to this post \| posted 20 Jan, 2018 19:43
debbie	Hi to all who have a Microbacterium phage! It is an exciting time in Actinobacteriophage discovery! We have learned that using comparative genomics to understand the genome content of each phage is profitable. It is great to compare your genome annotation(s) to genomes that have been previously called and QC'd. If you find that you are annotating a genome that has no final genome annotations with which to compare, do not go it alone! I have two considerations for you to follow: 1. You have much comparative data if there are draft genomes in the database. Do not ignore them. You will want to compare the genes and their starts using Phamerator, Starterator and other alignment tools. Do not ignore them simply because they are drafts. (Your evaluation will be different from a comparison to a final annotation, but the draft comparative data will inform your decision-making. In fact, Starterator will become your best friend! 2. Begin conversations with the owners of those drafts on the Forums to collaboratively work out the best annotations. Happy Annotating! Edited 22 Jan, 2018 18:35

Link to this post | posted 20 Jan, 2018 19:43

Hi to all who have a Microbacterium phage! It is an exciting time in Actinobacteriophage discovery! We have learned that using comparative genomics to understand the genome content of each phage is profitable. It is great to compare your genome annotation(s) to genomes that have been previously called and QC'd. If you find that you are annotating a genome that has no final genome annotations with which to compare, do not go it alone! I have two considerations for you to follow:
1. You have much comparative data if there are draft genomes in the database. Do not ignore them. You will want to compare the genes and their starts using Phamerator, Starterator and other alignment tools. Do not ignore them simply because they are drafts. (Your evaluation will be different from a comparison to a final annotation, but the draft comparative data will inform your decision-making. In fact, Starterator will become your best friend!
2. Begin conversations with the owners of those drafts on the Forums to collaboratively work out the best annotations.
Happy Annotating!

Edited 22 Jan, 2018 18:35

Link to this post \| posted 13 Mar, 2019 16:44
hkotturi	Hi, Just wanted to confirm this to see if I am on the right track. I have a student practicing annotation with Miaurora genome. It has already been annotated and submitted to GenBank. Miaurora has a frameshift in tail assembly chaperone (gene 10 and 11). My student is practicing documenting frameshifts. We generated a phamerator map with few close phage genomes (see attached image). So, if he were to work with HarperAnne_draft he would have to "add a gene" as gene 11 (with start and stop coordinates that would include Gene 10 Start and end with frameshift Stop). He would have to "add a gene" autoannotation in DNAMaster did not catch that extra part as shown in Owen_draft genome (gene 11). if he were to work with Owen_draft genome, he would follow the process described in the online guide (https://seaphagesbioinformatics.helpdocsonline.com/article-54) and just extend the start site for gene 11 as described on the webpage. am I right? Please let me know. 107Kb

Link to this post | posted 13 Mar, 2019 16:44

hkotturi

Hi,
Just wanted to confirm this to see if I am on the right track. I have a student practicing annotation with Miaurora genome. It has already been annotated and submitted to GenBank. Miaurora has a frameshift in tail assembly chaperone (gene 10 and 11). My student is practicing documenting frameshifts. We generated a phamerator map with few close phage genomes (see attached image).

So, if he were to work with HarperAnne_draft he would have to "add a gene" as gene 11 (with start and stop coordinates that would include Gene 10 Start and end with frameshift Stop). He would have to "add a gene" autoannotation in DNAMaster did not catch that extra part as shown in Owen_draft genome (gene 11).

if he were to work with Owen_draft genome, he would follow the process described in the online guide (https://seaphagesbioinformatics.helpdocsonline.com/article-54) and just extend the start site for gene 11 as described on the webpage.

am I right?

Please let me know.

Link to this post \| posted 14 Mar, 2019 01:39
debbie	Hari, Basically yes. However, when you add gene "11" in HarperAnne, add the gene only in that frame. If you add a gene that starts at 10 and ends at 11 it will be difficult to see where to slip it. (But if you know that coordinates of the slippage, it won't matter.) Then go back and chagen the start and add regions when you have it figured out. debbie

Link to this post \| posted 14 Mar, 2019 13:57
welkin	Hi Hari, IT looks like you are correct to me. Best, Welkin

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Annotations of Microbacterium foliorum