Link to this post | posted 13 Feb, 2018 18:24

cdshaffer

Unfortunately the last build of the SEA VM was done before I was able to release the version of Starterator with all the bug fixes. So the SEA VM version will work for many but not all phage. I have run a full phage report for Hegedechwinu on the updated version of starterator and you can download it from here: https://wustl.box.com/s/16md6n7clzkwz13xdvfpabxu8c28gjp5 Feel free to download and use. Be aware that what might work better for you is to use the pre-computed starterator reports. The nice thing about these reports is they are automatically updated with each new release of the phamerator database. These pre-computed pages are part of the effort to get away from the VM and get as much as possible available via web browser. These reports are available as links off of the phagesdb pages for the phams and the individual gene pages. Examples for pham 431: http://phagesdb.org/phams/431/ (Pham page, click on the blue “Get Starterator Report” button at the top of the page.) Example for gene 9 of phage Pollywog: http://phagesdb.org/genes/POLLYWOG_DRAFT_9/ (Gene page, click on the link “Pham 431 Report”, fourth row of the table.) Alternative methods for obtaining the reports are discussed on this forum page well. Edited 14 Feb, 2018 01:31

Link to this post | posted 13 Feb, 2018 18:00

cdshaffer

Not every gene that codes for a protein will show strong GeneMarkS potential. For a discussion of this see the forum page on Typical vs atypical GeneMarkS coding potential: https://seaphages.org/forums/topic/75/ But the bottom line is that Coding potential is based on looking at very long orfs in the genome itself to determine the sequence characteristics of a "typical" gene, it then uses that definition to score every region of the genome to indicate how closely it matches the "typical" result. Not all genes are expected to be "typical" so lack of coding potential is not good evidence for lack of a gene. See the discussion posted above for more details. As for Starterator, I have reposted your question to the Starterator section of the forum: https://seaphages.org/forums/topic/4500/ Edited 13 Feb, 2018 18:16

Link to this post | posted 13 Feb, 2018 17:54

cdshaffer

I am cross-posting this request for starterator help from grosasacosta below: I am having issues with Starterator. I've been trying to run it for Hegedechwinu but it keeps crashing when it reaches Pham 92 (near the end of the analysis). Any suggestion on how to solve this issue? It is related to that specific Pham. From what I saw in other similar posts, the solution may not be simple at all. Please let me know if you have any suggestions on how to solve this issue, I will be waiting. Edited 13 Feb, 2018 18:04

Link to this post | posted 08 Feb, 2018 23:30

cdshaffer

This is a general announcement that the starterator version used to create the pre-computed pham reports is being changed as of Feb 8th. This is necessary due to the ongoing work behind the scenes to improve the phamerator database. These changes to the database have necessitated updates to the methods starterator uses to determine if a phage should be considered a "draft" annotation. Most of the changes you will notice are cosmetic in nature, and feedback on these are always appreciated. More importantly, it is possible that the changes to the underlying code may have inadvertently introduced errors in determining if a phage is indeed "draft" quality. Please be on the lookout for errors of this type as you use the pham reports. If you find any examples which you believe may be in error please post these in this thread. Edited 09 Feb, 2018 17:28

Link to this post | posted 27 Jan, 2018 18:12

cdshaffer

According to the "Guiding Principles" I would say there is no lower cutoff. Context matters for interpretation of SD scores, for example, "If the genes are part of an operon, a 4bp overlap (ATGA), where a start codon overlaps the stop codon of the upstream gene, is preferred by the ribosome. Therefore RBS scores may have little bearing in this type of gene arrangement." Also, this: "The preferred start site usually has a favorable RBS score within all the potential start codons, but not necessarily the best. A notable exception is the integrase in many genomes, which has a very low RBS score. Our experimental data suggests that some genes do not have an SD sequence." {Bold added by me}

Link to this post | posted 26 Jan, 2018 02:25

cdshaffer

You can get to the starterator report from the gene page which might load more quickly than the pham page. If you know the pham number you can jump to the pham page at phagesdb by just adding /phams/# to the end of the url. For example to get the report for pham 123 just enter this in the address bar: phagesdb.org/phams/123 Also if you know the pham number you can just go directly to the starterator report. For example if you want to see the starterator report for pham 123 just type into the address bar: phages.wustl.edu/starterator/Pham123Report.pdf All reports have the same name except for the pham number section, so just substitute the 123 with your pham number. Another solution if you don't like typing out long URL's is to go to phages.wustl.edu/starterator You will get a list of all reports. Use your browser's find on this page, to search for the correct link.

Link to this post | posted 25 Jan, 2018 18:07

cdshaffer

It is technically possible to pre-computed whole phage reports for all phage but it is currently unfeasible. Whole phage reports take on average about 5 minutes on a decently powered computer and there are currently over 2300 phage. That works out to about 1 week to calculate all reports. Given that there is a new database every week means I would need 1 computer running full time and totally dedicated to the task. As for Starterator, there is the current "Stable" version that I used to create the report posted above. There is also an "Experimental" version that has a bunch of changes to the output. For comparison here is the output from the "experimental" version: Pollywog_DraftReport_experimental.pdf The experimental version has some improvements that I really like (e.g. sorting of the phage track to the top) that will certainly be in the next "Stable" release, but it also has some parts that still need work (e.g. like the new summary table) and will definitely be changing as soon as the semester calms down and I can get back to coding. Let me know which version you are interested in, and we can go from there.

Link to this post | posted 24 Jan, 2018 20:52

cdshaffer

Unfortunately the last build of the SEA VM was done before I was able to release the version of Starterator with all the bug fixes. So the SEA VM version will work for many but not all phage. I have run a full phage report for pollywog on the updated version of starterator and you can download it from here: Starterator report on Pollywog. Feel free to download and use but it may not be what would work best for you depending on your didactic goals. If you want include the use of VM's and Starterator in your class then it is probably best to update the VM with the latest version of starterator. It is fairly straight forward, just post a follow-up query on how to update starterator if you are interested. Another alternative is to use the pre-computed starterator reports. This is part of the effort to get away from the VM and get everything available via web browser so it is platform independant. These reports are available as links off of the phagesdb pages for the phams and the individual gene pages. Examples: http://phagesdb.org/phams/431/ (Pham page, click on the blue “Get Starterator Report” button at the top of the page.) http://phagesdb.org/genes/POLLYWOG_DRAFT_9/ (Gene page, click on the link “Pham 431 Report” link in the fourth row of the table.) The good part about these pre-computed reports is that they are updated every time new phage genomes are added to the phamerator database throughout the spring. The whole phage report above may get out of date if more F1 phages are sequenced and added to the database.

Link to this post | posted 10 Jan, 2018 22:26

cdshaffer

DNA Master prefereces must now be updated to use the PBI servers specific for SEA-PHAGES courses. See the help document, it is in the faculty only -> faculty info page, in the Bioinformatic Component section. The link is called "DNA Master Gene Prediction Settings", it describes how to change a few preference settings in DNA Master to get auto annotation working. If you followed those instructions and it is still failing, check your internet connection.

Link to this post | posted 10 Jan, 2018 19:58

cdshaffer

Yes, I think you are correct. I have found DNA Master to be a bit finicky. I had one student last semester with a mac and we were never able to get it to run successfully even though it was running just fine on all the other macs in the class. Like you, we tried deleting everything and reinstall several times with no luck, it just never worked on that one mac. I tried to replicate your issue on my mac and was able to import and auto-annotate a C phage, so like my one student you are probably doing everything correctly and it is just something with the macs you are using. The only suggestions I have, give that the issue only appears with larger genomes, would be to try macs with more memory, it's a long shot but might work.