SEA-PHAGES | Glimmer Failure on Auto Annotation

Link to this post \| posted 02 Aug, 2017 15:44
smg366	Thank you this, I was having trouble with the auto-annotate as well but have resolved it using PECAAN. Thanks!

Link to this post \| posted 04 Aug, 2017 15:45
NWCiowaSEAPHAGE	Hi Chris, I've got an account with PECAAN - thanks! I think I'll use some of it this semester. I've exported the GenBank file and saved it. When I open it in DNA Master it flickers up and then disappears…The first date I need the DNA Master file is August 24th so it's not truly urgent yet. However, I'm not sensing an easy solution is coming really soon so it you don't mind, I'd love to take you up on your offer to get a DNA master file for Roots515. Many thanks! I'm not sure how you will get that file to me but in case it is by email I'm at stolsma@nwciowa.edu. - Sara cdshaffer It is not you or your system. I am getting the same result. It looks like NCBI is no longer serving glimmer and genemark analysis as a web page (which is what DNA Master used) and is now forwarding all web requests for those pages to the download pages of the software. This totally breaks DNA Master auto-annotation as you have discovered. A long term solution is going to require updates to DNA Master. In the short term, it is probably easiest to use PECAAN. You can start here: https://seaphages.org/forums/topic/224/ Which explains how to get an account and a link to the user guide. PECAAN is under very active development so the user guide will help get you started but expect the actual web pages to be different. Pecaan is nice in that it will do a lot of the drudgery of entering notes in a proper format if you use it to do all your annotations. So you may want to consider switching over to using it for a lot of the annotation work. If you are in a huge hurry (like you need the DNA Master file ASAP for a class) just post the name of the phage I can use pecaan to generate the auto-annotation file for you very easily. If you want to try to use pecaan to do most of your annotation, feel free to post any follow=up questions to the PECAAN section of the forum.

Link to this post | posted 04 Aug, 2017 15:45

NWCiowaSEAPHAGE

Hi Chris,
I've got an account with PECAAN - thanks! I think I'll use some of it this semester. I've exported the GenBank file and saved it. When I open it in DNA Master it flickers up and then disappears…The first date I need the DNA Master file is August 24th so it's not truly urgent yet. However, I'm not sensing an easy solution is coming really soon so it you don't mind, I'd love to take you up on your offer to get a DNA master file for Roots515. Many thanks! I'm not sure how you will get that file to me but in case it is by email I'm at stolsma@nwciowa.edu.
- Sara

cdshaffer
It is not you or your system. I am getting the same result. It looks like NCBI is no longer serving glimmer and genemark analysis as a web page (which is what DNA Master used) and is now forwarding all web requests for those pages to the download pages of the software.
This totally breaks DNA Master auto-annotation as you have discovered. A long term solution is going to require updates to DNA Master.

In the short term, it is probably easiest to use PECAAN. You can start here:

https://seaphages.org/forums/topic/224/

Which explains how to get an account and a link to the user guide. PECAAN is under very active development so the user guide will help get you started but expect the actual web pages to be different. Pecaan is nice in that it will do a lot of the drudgery of entering notes in a proper format if you use it to do all your annotations. So you may want to consider switching over to using it for a lot of the annotation work.

If you are in a huge hurry (like you need the DNA Master file ASAP for a class) just post the name of the phage I can use pecaan to generate the auto-annotation file for you very easily.

If you want to try to use pecaan to do most of your annotation, feel free to post any follow=up questions to the PECAAN section of the forum.

Link to this post \| posted 18 Aug, 2017 17:56
debbie	Right now, you cannot auto-annotate in DNA Master. We are working at getting Glimmer and GeneMark onto servers to send DNA Master to. That should not be difficult but isn’t available yet. I'll keep you posted! If you are ready to auto-annotate now – I recommend using PECAAN. There are 2 ways to do it. Use the full suite of PECAAN functions and upload the files there. Once the genes are called, you can download a genbank file that uploads nicely into DNA Master. If you don’t want to use all of PECAAN, Claire Rinehart & Co. also created an auto-annotation tool that outputs the documentation of auto-annotation that can be pasted in the documentation window of newly created dnam5 file made from a FASTA input. (Claire commented on the difference between the 2: When the genome is loaded into PECAAN, the program will predict the genes but also do the BLAST for each gene. This can take some time and is system intensive. When the genome is loaded into the auto annotate tool, it only calls the gene and has less impact on our computing system. Therefore, if people don’t need the BLAST and HHPred results, please have them use the auto annotate tool.) IF YOU DO USE PECAAN, YOU CAN ONLY USE IT ONLY ONCE PER GENOME. So if you want the whole classroom to do this, use the auo-annotation tools for your students. If that doesn’t make sense, ask me again and I will explain. https://discover.kbrinsgd.org/evidence/summary https://discover.kbrinsgd.org/autoannotate/ It is quite the work-around, but it does get the job done. Edited 18 Aug, 2017 17:57

Link to this post | posted 18 Aug, 2017 17:56

debbie

Right now, you cannot auto-annotate in DNA Master. We are working at getting Glimmer and GeneMark onto servers to send DNA Master to. That should not be difficult but isn’t available yet. I'll keep you posted!

If you are ready to auto-annotate now – I recommend using PECAAN. There are 2 ways to do it. Use the full suite of PECAAN functions and upload the files there. Once the genes are called, you can download a genbank file that uploads nicely into DNA Master. If you don’t want to use all of PECAAN, Claire Rinehart & Co. also created an auto-annotation tool that outputs the documentation of auto-annotation that can be pasted in the documentation window of newly created dnam5 file made from a FASTA input. (Claire commented on the difference between the 2: When the genome is loaded into PECAAN, the program will predict the genes but also do the BLAST for each gene. This can take some time and is system intensive.
When the genome is loaded into the auto annotate tool, it only calls the gene and has less impact on our computing system. Therefore, if people don’t need the BLAST and HHPred results, please have them use the auto annotate tool.) IF YOU DO USE PECAAN, YOU CAN ONLY USE IT ONLY ONCE PER GENOME. So if you want the whole classroom to do this, use the auo-annotation tools for your students.

If that doesn’t make sense, ask me again and I will explain.

https://discover.kbrinsgd.org/evidence/summary

https://discover.kbrinsgd.org/autoannotate/

It is quite the work-around, but it does get the job done.

Edited 18 Aug, 2017 17:57

Link to this post \| posted 18 Aug, 2017 22:14
cdshaffer	just to document for anyone what wants to create an auto-annotation here is what I did: 1. open DNA Master and do the standard File -> Open Fasta and import the sequence 2. Go go https://discover.kbrinsgd.org/autoannotate/ and enter phage name and upload the same sequence file you used in step 1 3. Click "Process" 4. In the text box below the process button you will get the auto-annotation as "Documentation"; it will have a bunch of entries that look something like this: `CDS 15 - 272 /gene="1" /product="gp1" /locus tag="Roots515_1"` 5. Select and Copy the entire contents of that text box 6. Go back to DNA master, on the phage window click the "Documentation" tab at the top right 7. Delete any text in the large text box and paste in from the results from the PECAAN auto-annotation. (When I did this this step I got about 100 question marks at the end which I deleted so the last entry ended like this: `CDS join(155929. .156288;1. .1 /gene="232" /product="gp232" /locus tag="Roots515_232" /note=Original Glimmer call @bp 155929 has strength 11.01 ** not called by GeneMark` 8. click the parse button, then in the window that opens accept the defaults and click the new parse button. This will convert the "documentation" into DNA Master gene entries 9. Save the DNA Master file as usual Edited 18 Aug, 2017 22:22

Link to this post | posted 18 Aug, 2017 22:14

cdshaffer

just to document for anyone what wants to create an auto-annotation here is what I did:

1. open DNA Master and do the standard File -> Open Fasta and import the sequence
2. Go go https://discover.kbrinsgd.org/autoannotate/ and enter phage name and upload the same sequence file you used in step 1
3. Click "Process"
4. In the text box below the process button you will get the auto-annotation as "Documentation"; it will have a bunch of entries that look something like this:

CDS 15 - 272
  /gene="1"
  /product="gp1"
  /locus tag="Roots515_1"

5. Select and Copy the entire contents of that text box
6. Go back to DNA master, on the phage window click the "Documentation" tab at the top right
7. Delete any text in the large text box and paste in from the results from the PECAAN auto-annotation. (When I did this this step I got about 100 question marks at the end which I deleted so the last entry ended like this:

CDS join(155929. .156288;1. .1
  /gene="232"
  /product="gp232"
  /locus tag="Roots515_232"
    /note=Original Glimmer call @bp 155929 has strength 11.01 ** not called by GeneMark

8. click the parse button, then in the window that opens accept the defaults and click the new parse button. This will convert the "documentation" into DNA Master gene entries
9. Save the DNA Master file as usual

Edited 18 Aug, 2017 22:22

Link to this post \| posted 18 Aug, 2017 22:18
NWCiowaSEAPHAGE	I got it to work this afternoon, actually! ! It's BLASTING as I type this

Link to this post \| posted 19 Aug, 2017 01:58
smg366	NWCiowaSEAPHAGE I got it to work this afternoon, actually! ! It's BLASTING as I type this Were you able to get BLAST to work? I have been trying to BLAST my genome in DNA Master for the past few days and it has not worked. I was wondering if this was specific to my computer or the program.

Link to this post \| posted 19 Aug, 2017 17:46
NWCiowaSEAPHAGE	I checked in this morning and my BLAST went just fine (and it was a large genome - over 150 kB). I'm not sure what to suggest. I'm no computer wiz. I kind of limp along and learn as I go. smg366 NWCiowaSEAPHAGE I got it to work this afternoon, actually! ! It's BLASTING as I type this Were you able to get BLAST to work? I have been trying to BLAST my genome in DNA Master for the past few days and it has not worked. I was wondering if this was specific to my computer or the program.

Link to this post | posted 19 Aug, 2017 17:46

NWCiowaSEAPHAGE

I checked in this morning and my BLAST went just fine (and it was a large genome - over 150 kB). I'm not sure what to suggest. I'm no computer wiz. I kind of limp along and learn as I go.

smg366
NWCiowaSEAPHAGE
I got it to work this afternoon, actually! ! It's BLASTING as I type this

Were you able to get BLAST to work? I have been trying to BLAST my genome in DNA Master for the past few days and it has not worked. I was wondering if this was specific to my computer or the program.

Link to this post \| posted 29 Aug, 2017 19:59
Tamarah_Adair	Thank you Chris for posting those instructions and Claire and all for making this available. This is great!

Link to this post \| posted 01 Sep, 2017 17:28
svoshell	Chris, thank you for providing the instructions. It's such a simple fix, but I would have been panicking for days if I hadn't found this post!

Link to this post \| posted 03 Oct, 2017 18:28
Tamarah_Adair	When we ran Yeezus through Pecaan using the autoannotate tool, it did not return the full genome. Is there a work around for this? Also, when we open the Starterator file for Yeezus, the gene numbers are not lining up with the DNAMaster file made using the documentation from Pecaan. Any ideas there? Thanks!

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Glimmer Failure on Auto Annotation