Link to this post | posted 29 Jan, 2020 22:27
cdshaffer	To adjust the VM desktop image use the virtual box View -> Virtual Screen -> Scale to… menu item. When I am on a high res screen like my macbook pro screen I set "Scale to 200%" and when I am on an external monitor I set "Scale to 100%" but feel free to pick whatever scale works best for you.

Link to this post | posted 21 Jan, 2020 23:15
cdshaffer	The picture you posted looks like you are running an old version of DNA Master. Mine version of that tab looks like the attached. You should double check that you have an up to date version of DNA Master. I just checked and it says: Version 5.23.3 build 2693 from 26 November 2019 which it reports is up to date. 27Kb

Link to this post | posted 21 Jan, 2020 23:06

cdshaffer

With the MLK holiday weekend I was not able to calculate the new reports until this afternoon for the recently posted version of the database. The reports for this release of the database (number 336) has now been posted and pham 106383 is now available. Most missing phams are due to this issue of databases being out of sync. Unfortunately, it takes up to 20 CPU hours to calculate all 14,000 or so Starterator reports. Thus Starterator will typically be the last to update and often up to 1 day later than the other web pages. You can see which version of the database PECAAN is using on the PhamMaps page just above the map; for phamerator.org you can see which version in the pull-down menu near the top left corner; for Starterator the database version is now indicated near the top of the second page just after the date run. If these numbers do not match you can expect a higher risk of missing phams until the new Starterator analysis has been posted.

Link to this post | posted 18 Dec, 2019 00:12

cdshaffer

Sorry about that. Yes, you unfortunately got stuck in the awkward time between when the new version of the database gets uploaded and all the Starterator reports get published to the web. Starterator has the most processing to do on each pham so it will always be the last piece to update. I was able to push the most recent reports to the server late this morning after an overnight run. As the database grows it is taking longer and longer to process all those pham reports and it is now often taking up to 1 full day to get things uploaded. Edited 18 Dec, 2019 00:14

Link to this post | posted 09 Dec, 2019 19:35
cdshaffer	it does not appear that the large overlap is found in the BD2 cluster. Large overlap is found in most other subclusters. Edited 10 Dec, 2019 16:13

Link to this post | posted 15 Nov, 2019 21:24

cdshaffer

This is to announce the release of Starterator version 1.2 This release has some graphical updates and incorporates cluster information into the text reporting. The cluster information can be particularly helpful for large complex phams but has little or no value for small phams comprised of a single cluster. The new version will be used to create all online pham reports starting with database version 233 which should be posted to the web based pham reports the afternoon of Nov 15th. For anyone still using the virtual machine the new version will be made available soon for download and update (details to be posted soon). The main new features in this update: 1. Tracks now display only that region of the genes with starts, and, if the tracks are judged to be highly complex, the image is further zoomed in to show only the region surrounding called start sites 2. Tracks are now grouped by subcluster and the color of the track changes with each subcluster (Thanks for the idea go to Sally Molloy) 3. Cluster information of each phage is now added to the "Summary by Start" section (Thanks for the feature request go to Claire Rinehart) 4. A new "Summary by cluster" section has been added to give info on manual annotations specifically for each cluster found in the pham 5. Details on the number of manual annotations (MA's) for each start in a gene are now given in the "Gene information" section. Also added to the whole phage report (available if you still run starterator in a VM): 6. A new summary table on the analysis of manual annotations of pham members and the degree of consensus with the annotated start. 7. Simplified reporting focusing on the relevant results for the phage in the whole phage report 8. Support for parsing of the "CDS function" file exported from Pecaan when using the whole unphamerated phage analysis

Link to this post | posted 03 Oct, 2019 16:10
cdshaffer	down for me as well when since last Monday

Link to this post | posted 01 Oct, 2019 14:53

cdshaffer

You can get the translations of any gene using /api/genes/{GeneID}/ but the API returns everything in JSON format not FASTA format and you would have to do them one at a time. As an example if you want the info on gene 1 of phage Dori call this URL: https://phagesdb.org/api/genes/Dori_CDS_1/ in the results you will get the amino acid sequence in the "translation". Another alternative, although more manual, would be to use the "Download all sequences" button on the pham page of phagesdb. This will give you all the protein sequences of all members of the pham in FASTA format. Depending on your exact goal this might be good enough, you just need to figure out which phams you want and decide if all pham members are appropriate for your purpose. Finally, if you have a specific gene list and you want all the sequences programmatically, you could consider using the phamerator database and use mysql to query the database based on gene names; the data you want is in the gene table in the translation field. You could get to that data by either using a graphical user interface or the command line. Edits December 2021: the name of the gene has changed from Dori_1 to Dori_CDS_1; URL was updated. The current names of the genes are available from the "genesbyphage" request i.e. https://phagesdb.org/api/genesbyphage/Dori ) Edited 30 Dec, 2021 00:18

Link to this post | posted 07 Aug, 2019 19:10

cdshaffer

I believe the "major" and "minor" terms relate back to very early papers where they purified phage proteins and ran them out on protein gels. So a "major" proteins would be the very intense band on the gel and would presumably be high copy number. There would also be weak or even very faint banks on the gel and these would be the "minor" proteins. The terms then had less to do with size but rather abundance.

Link to this post | posted 05 Aug, 2019 22:30

cdshaffer

I always think that an HHPRED of 100% probability is an indication that it is very confident that the protein you are searching with belongs to the same family of proteins it is matching. Chitin is a polymer of β-(1→4)-linkages of N-acetylglucosamine (NAG) while peptidoglycan is alternating residues of β-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid. I always try to remind my students that functional annotation down to one specific substrate is very risky. In my mind it is easy to change just one or two amino acids at exactly the right place to radically change the binding properties of an enzyme to any one specific substrate. And one should be even more careful when there are known to be many different but related substrates [like polysaccharides]. So annotation of this type needs a "sanity check". Does it make sense that a phage would have an enzyme that cleaves chitin? No, not really, so I would not annotate this as a chitinase. One the other hand, it does make sense that some ancient protein that does something with N-acetylglucosamine could easily evolve into a chitinase along one branch and evolve into some other protein that somehow interacts with peptidoglycan in another branch. I would come away pretty confident that this phage protein either binds to NAG or cleaves β-(1→4)-linkages of NAG. Since there is no approved term for "protein either binds to NAG or cleaves β-(1→4)-linkages of NAG" I would stick with "minor tail protein" but I would also be pretty confident of that annotation given the structural similarity of chitin and peptidoglycan.