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All posts created by cdshaffer

| posted 24 Jul, 2020 22:15
Wow, somehow I missed this message, sorry about that.
Yes starterator is still being updated but it often lags behind the other pages. The issue is that right now the Hatfull lab is working on a large refactoring of the database and while these changes are on going all the web pages are much more likely to get out of sync.

Exactly which version of the database each web page is on varies. I think phagesdb and phamerator are on version 362 while pecaan and starterator are on version 364. So if you are using pecaan things should work OK but if you are looking for phams based on phagesdb or phamerator.org you need to go to an older version of the starterator reports. To do that just substitute the "starterator" part of the URL with the database number, so to get pham 8041 from database version 362 go to:

http://phages.wustl.edu/362/Pham8041Report.pdf


And Voilà you have your report. Since most phams stay the same across releases most links from phagesdb should work, but when they don't just substitute in the "362" into the URL. This will work until phagesdb is updated to the current version, at which point all links should work.
Posted in: StarteratorPham not found in Starterator
| posted 19 Jun, 2020 17:47
I guess the answer depends on exactly what you are looking for in your comparison.

DNA master has a nice comparison tool if you only want to check a small number of genomes like you mention. Just like phamerator it will compare predicted protein sequences and group similar proteins into a single group that it assigns a unique color. The algorithm for comparison is not the exact same as phamerator so you get a "different but similar" kind of grouping but if all your phage are in the same subcluster it works pretty well. You will need DNA Master files of all the phage.

The DNA master protocol works really well for gene content analysis and moderately well if you are trying to see if you have called the same start sites as your comparison phage but for the later I have now switched to using the whole phage starterator report which I think is much better at doing a check of start codon choices. If you want a whole genome starterator please check out this thread: https://seaphages.org/forums/topic/4998/
It is trivially easy for me to set the run up and post the results, so always happy to run the analysis.
Posted in: PhameratorPhamDB: Make your own Phamerator databases
| posted 11 Jun, 2020 21:25
as the pham number is likely to change, here is the link to the Lokk gene 39 to check the current pham number: Lokk_CDS_35

P.S remember gene numbers can change by annotation and whether you are counting tRNA genes as well as protein genes. so confirming genes by coordinates is always recommended.
Posted in: Cluster A Annotation TipsPham 23651 function assignment
| posted 09 Jun, 2020 14:41
The list of all the hosts can be found here:

https://phagesdb.org/hosts/

Unfortunately, Myocobacterium marinum does not appear on the mycobacterium sub-list.
Posted in: MycobacteriumMycobacterium Marinum
| posted 21 May, 2020 16:18
Database creation takes A LOT of computation and scales up exponentially with the number of phage.
Are you just working with 18 phage or did you add 18 phage to a larger database?
With 18 phage I would expect it to take at least a few minutes maybe up to 10, if you are adding phage to something larger it could take several hours to overnight. The last time I did this with ~100 phage on a pretty powerful computer it took over 2 hours.

The best way to get feedback and know if it is probably working is to use the utility in your OS that tells you how hard your CPU is working (either Activity Monitor on Mac or Task Manager in Win). If your phamdb is set up correctly, after you click the button you should see your CPU usage spike up and stay busy.
Posted in: PhameratorPhamDB: Make your own Phamerator databases
| posted 16 May, 2020 18:39
NCBI is quite restrictive in running BLAST searches that are submitted by computer programs like DNA Master and not submitted by individuals using the web interface. NCBI is really just not able to keep up with all the blast searches everyone around the world wants and so these automatically submitted searches are getting more and more restrictive. Your BLAST searches at NCBI do not stop if you quit DNA Master, so every time you retry the searches you add more and more searches to your queue and there is a limit to how many searches you can do at any one time. Given you have tried 7 times this is probably why you are getting this "Too many outstanding requests" error. According to the DNA Master settings it will submit 25 searches at a time so you may have submitted up to 175 searches if DNA master really did submit 25 searches each of those 7 times.

According to the rules on this page: "We will move searches of users who submit more than 100 searches in a 24 hour period to a slower queue, or, in extreme cases, will block the requests. "

Given that you used PECAAN all the blast results are available to any one who is checking your annotations, so i would suggest you go ahead and submit your DNA Master file without redoing the BLAST results and just note in the cover sheet the issues you had with NCBI and that the BLAST results are available in PECAAN.
Posted in: PECAANProblem BLASTING after PECAAN file transferred to DNA Master
| posted 27 Apr, 2020 00:44
yes, two trivial things to try, 1) try a different browser sometimes this helps. 2) maximize the window size on the browser to fill the screen. 3) set zoom level to less than 100%, 4) Move to a computer with a large screen and try there (these problems usually show up on portables with small 12 or 13 inch screens). I never have had an issue in my office with my large 24 inch monitor
Posted in: PECAANproblem with adding a gene
| posted 26 Mar, 2020 18:30
missing or broken links are almost always due to pham changes with each new database release.
New databases typically come out at least once a week.
Once a database has been released by the Hatfull lab it takes each subsystem a variable amount of time to update. phagesdb.org will update almost immediately since it is also in the Hatfull lab. Phamerator.org and Pecaan will typically update pretty quickly as all they need to do is download and install the new database. Starterator will almost always update last as it takes quite a bit of time to run 15,000 clustal alignments and create the 15,000 reports.

Phamerator.org, pecaan and starterator all have a way to see which database version they are on:
phagesdb see: http://phamerator.webfactional.com/databases_Hatfull/Actino_Draft.version
starterator see: http://phages.wustl.edu/starterator/database.version
pecaan: look on any "pham maps" page just above the map
phamerator.org: open the pull down menu in the top left
Posted in: PECAANCould this Pham be improperly assigned in PECAAN?
| posted 18 Mar, 2020 03:34
This is a database synchronization issue. Phagesdb was on version 347 and the other sites were behind. This can happen anytime a new database is released. It takes a variable amount of time for each site to "catch up". Starterator usually takes about a day as there is a lot of computer work to calculate ~15000 multiple sequence alignments and generate ~15,000 reports, but it is now up to date and should give the correct results. Not sure about PECAAN or phamerator.org. The first thing you should try when you get these discrepancies is check which database each site is on.If they are on different versions

This is how you can get the info on which version each site is on:
phagesdb see: http://phamerator.webfactional.com/databases_Hatfull/Actino_Draft.version
starterator see: http://phages.wustl.edu/starterator/database.version
pecaan: look on any "pham maps" page just above the map
phamerator.org: open the pull down menu in the top left
Posted in: StarteratorPhage not found in track
| posted 17 Mar, 2020 18:37
I just searched the phamerator database. There are no genes from amy phage with host streptomyces that have lysin B as an annotation.
Posted in: Cluster BD Annotation Tipslysin A