SEA-PHAGES | Conserved Domain ID in notes

Link to this post \| posted 11 Feb, 2016 16:46
fbaliraine	What does "Conserved Domain ID - NCBI" and "Conserved Domain ID - Phamerator" mean in the annotation notes in DNA Master? Does it mean the accession number? See example in attached figure.I have looked at pages 109-110 in the DNA Master Guide 2016 but did not see the domain ID mentioned. Thanks! 155Kb

Link to this post \| posted 16 Feb, 2016 18:46
welkin	It does not mean accession number. The conserved domain database is part of NCBI and is searched by default when you BLAST a protein against GenBank through your browser rather than through DNA Master. If you have a CDD match, you will see a separate page with your CDD results, like in your attached figure. For this result, you would write "CDD, phage capsid". Phage capsid is the domain ID. You can also see CDD matches in Phamerator (the yellow boxes that appear on your genome map in your genes that you can browse over).

Link to this post | posted 16 Feb, 2016 18:46

welkin

It does not mean accession number. The conserved domain database is part of NCBI and is searched by default when you BLAST a protein against GenBank through your browser rather than through DNA Master. If you have a CDD match, you will see a separate page with your CDD results, like in your attached figure. For this result, you would write "CDD, phage capsid".
Phage capsid is the domain ID.
You can also see CDD matches in Phamerator (the yellow boxes that appear on your genome map in your genes that you can browse over).

Link to this post \| posted 03 Mar, 2016 23:30
GregFrederick@letu.edu	So are CDDs the number that is associated with the features in Phamerator? (Not the number hovering above each feature? What are these numbers, BTW?) Some of the yellow boxes have actual gene functions. So am I right that those do not have CDDs listed?

Link to this post \| posted 16 Feb, 2017 15:48
GregFrederick@letu.edu	Welkin: One more question on this. The CDD is to be listed in the notes section within DNA Master under the FS: If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"? Thanks again for your input. We are just wanting to get everything done correctly "the first time" and obviously we have a bit of confusion on a few things… Thanks. Greg

Link to this post | posted 16 Feb, 2017 15:48

GregFrederick@letu.edu

Welkin: One more question on this.

The CDD is to be listed in the notes section within DNA Master under the FS:

If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?

Thanks again for your input. We are just wanting to get everything done correctly "the first time" and obviously we have a bit of confusion on a few things…

Thanks. Greg

Link to this post \| posted 16 Feb, 2017 16:08
GregFrederick@letu.edu	Welkin (or whomever): See question above. But I have one more… If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well? Thanks again.

Link to this post \| posted 16 Feb, 2017 22:36
cdshaffer	Most of your questions are more about the policy for good notes so I will leave those to the more informed, but I can answer the question about the numbers in phamerator hover above the genes. If you are on phamerator.org the number is the phamily number. If you are using the maps from the stand alone version of phamerator from the SEA VM there is a second number inside parentheses that is (the number of proteins in the phamily).

Link to this post | posted 16 Feb, 2017 22:36

cdshaffer

Most of your questions are more about the policy for good notes so I will leave those to the more informed, but I can answer the question about the numbers in phamerator hover above the genes. If you are on phamerator.org the number is the phamily number. If you are using the maps from the stand alone version of phamerator from the SEA VM there is a second number inside parentheses that is (the number of proteins in the phamily).

Link to this post \| posted 21 Feb, 2017 22:36
GregFrederick@letu.edu	Hi guys. I still need input on these questions (from above). If you would prefer to call me my number is 903.233.3354 or my email address is GregFrederick@letu.edu QUESTION 1: "If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?" QUESTION 2: "If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well?" HHPed? Thanks for your help with this… I appreciate it. Greg

Link to this post | posted 21 Feb, 2017 22:36

GregFrederick@letu.edu

Hi guys.

I still need input on these questions (from above). If you would prefer to call me my number is 903.233.3354 or my email address is GregFrederick@letu.edu

QUESTION 1: "If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?"

QUESTION 2: "If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well?" HHPed?

Thanks for your help with this… I appreciate it. Greg

Link to this post \| posted 21 Feb, 2017 22:38
GregFrederick@letu.edu	GregFrederick@letu.edu Hi guys. I still need input on these questions (from above). If you would prefer to call me my number is 903.233.3354 or my email address is GregFrederick@letu.edu QUESTION 1: "If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?" QUESTION 2: "If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well?" HHPed? Thanks for your help with this… I appreciate it. Greg Sorry for the repeat posts. We are just about done with the annotation phase and really want to be certain we have done everything required. Thank you.

Link to this post | posted 21 Feb, 2017 22:38

GregFrederick@letu.edu

GregFrederick@letu.edu
Hi guys.

I still need input on these questions (from above). If you would prefer to call me my number is 903.233.3354 or my email address is GregFrederick@letu.edu

QUESTION 1: "If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?"

QUESTION 2: "If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well?" HHPed?

Thanks for your help with this… I appreciate it. Greg

Sorry for the repeat posts. We are just about done with the annotation phase and really want to be certain we have done everything required. Thank you.

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Conserved Domain ID in notes