Link to this post | posted 17 Jan, 2018 17:39

ClaireRinehart

Dan, I try regularly to update our function list in PECAAN so that it matches the Official Function List here at SEA PHAGES (https://seaphages.org/blog/2017/10/30/official-function-list/). I noticed that you have a line at the top of the page: Written by Dan Russell on Oct. 30, 2017 . My question is this, does this date change whenever you update the list? If not, then could you put a "Last Updated" cell in the sheet itself that will give me something to monitor? -Claire

Link to this post | posted 11 Aug, 2017 13:55

ClaireRinehart

In the annotation of Biglebops_31 (27784-28920) we found multiple hits to endonucleases (Hammy_34, Vendetta_66, Splinter_66) and to exonucleases LindNT_35, Marcoliusprime_34), all with e-values of 0. HHPRED also had several hits to endo- and exo-nucleases as well as hits to MRE11 which has both activities and is a DNA double-strand break repair protein (99.5% probability, 60-70% coverage and e-values 10^-12 to 10^-14) that pairs with RAD50, an ATPase. We have no accepted annotation that would best fit this situation. Could we add a "DNA double strand break repair, Mre11-like protein" annotation function to our accepted list? I have included below, an associated paper abstract for the top hit 1ii7_A that explains the relationship of Mre11 and Rad50. Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Hopfner, K.P., Karcher, A., Craig, L., Woo, T.T., Carney, J.P., Tainer, J.A. (2001) Cell(Cambridge,Mass.) 105: 473-485 PubMed: 11371344 Search on PubMed Primary Citation of Related Structures: 1II7 1II8 PubMed Abstract: To clarify functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair, we report Pyrococcus furiosus Mre11 crystal structures, revealing a protein phosphatase-like, dimanganese binding domain capped by a unique domain controlling active site access. These structures unify Mre11's multiple nuclease activities in a single endo/exonuclease mechanism and reveal eukaryotic macromolecular interaction sites by mapping human and yeast Mre11 mutations. Furthermore, the structure of the P. furiosus Rad50 ABC-ATPase with its adjacent coiled-coil defines a compact Mre11/Rad50-ATPase complex and suggests that Rad50-ATP-driven conformational switching directly controls the Mre11 exonuclease. Electron microscopy, small angle X-ray scattering, and ultracentrifugation data of human and P. furiosus MR reveal a dual functional complex consisting of a (Mre11)2/(Rad50)2 heterotetrameric DNA processing head and a double coiled-coil linker. Edited 11 Aug, 2017 13:59

Link to this post | posted 31 Jul, 2017 15:50

ClaireRinehart

Just a note to update you on some of the latest features added to PECAAN. Whenever you begin to type a function into PECAAN it will show you all of the matching functions that are found in the "approved function list". An easy way to take advantage of this feature is to type in all of part of the root function and then select the appropriate function from the drop-down list. With the initiative to only enter "approved functions" we have also included an indicator of membership in the "approved function list" in the gene number selection drop-down at the top of the Genes window. If a function is on the "approved function list" then a green checkmark will appear before the gene number. If a function is not on the "approved function list" then a red x will appear before the gene number. This should help in reviewing whether the functions, that have been entered for the genes, have the correct description. We have also added a Function option, under the Admin menu item, that allows SuperAdmin users to modify and update the approved function list.

Link to this post | posted 31 Jul, 2017 15:33

ClaireRinehart

Thanks Welkin. I added "membrane protein" back into the PECAAN approved function list. Dex added a new feature to PECAAN in the drop-down that is used to select gene numbers. If there is a green check before the gene number then you know that the designated function is in the approved list. If a red x is showing before the gene number then the designated function is not a member of the approved function list. This saved me an hour last week when I was reviewing functions and their conformation to the approved function list.

Link to this post | posted 27 Jul, 2017 20:29

ClaireRinehart

I was updating PECAAN's Function field automatch list today and found that the "membrane protein" notation has been dropped. We added the TMHMM transmembrane predictor to PECAAN in response to Debbie indicating that there were several membrane proteins located in a specific region of the Arthobacter genomes. We found these same membrane proteins in our Arthrobacter phage and thought that it would be nice to have this as a PECAAN feature. Knowing that a protein is predicted to be located in the membrane is useful to identifying some functions such as holins while at other times it is not known how this feature contributes to the function but may be found fairly consistently, such as in tape measure proteins. I would like to see this general function feature returned to the approved list, perhaps as "predicted membrane protein" because it brings a lot of functional potential to the annotation table that "hypothetical protein" just does not.

Link to this post | posted 05 Jul, 2017 22:17

ClaireRinehart

Lee Hughes and his students pointed out that when quotes were entered into the notes section of PECAAN and then the data was exported to DNA Master that the text imported into the Notes field in DNA Master were truncated at the first quote. Therefore, putting 5' or 3' designations into the notes would cause truncations. We tried additional testing and also found that when we put CR-LF (carriage return & line feed symbols) into the notes during our PECAAN GenBank format export that DNA Master also truncated the GenBank import at the first CR-LF. We tried importing PECAAN's GenBank export into Geneious and found no truncations with either the quotes or the CR-LF. This appears to be a DNA Master-specific quirk (or bug). We are therefore removing the CR-LF from the GenBank export and substituting ` for ' in all other exports from PECAAN.

Link to this post | posted 05 Jul, 2017 22:15

ClaireRinehart

Lee Hughes and his students pointed out that when quotes were entered into the notes section of PECAAN and then the data was exported to DNA Master that the text imported into the Notes field in DNA Master were truncated at the first quote. Therefore, putting 5' or 3' designations into the notes would cause truncations. We tried additional testing and also found that when we put CR-LF (carriage return & line feed symbols) into the notes during our PECAAN GenBank format export that DNA Master also truncated the GenBank import at the first CR-LF. We tried importing PECAAN's GenBank export into Geneious and found no truncations with either the quotes or the CR-LF. This appears to be a DNA Master-specific quirk (or bug). We are therefore removing the CR-LF from the GenBank export and substituting ` for ' in all other exports from PECAAN.

Link to this post | posted 21 Jun, 2017 19:41

ClaireRinehart

The Starterator field in PECAAN is a legacy field to accommodate manual entry from an edited Starterator report that we don't encourage use of anymore. The best way to view the Starterator information is by clicking on the Pham link. This loads a Starterator summary that is very useful. After clicking on the Pham link, scroll down to the text: "Summary of Final Annotations (Info on gene starts based on numbers in diagram): The start number called the most often in the published annotations is start number" X, where X is the most published start number, as displayed in the tracks (map at the top). This is the number that Staterator recommends. (Helpful navigation hint: Using the Find command for your machine will help you navigate to find information for your specific phage. Type your phage name into the Find field (activated by command F on the Mac) and press the keys (command G on the Mac) to find the next instance of your phage name in the text.} Next, there are three classifications for genes: Genes that call this "Most Annotated" start. Genes that have the "Most Annotated" start but do not call it. Genes that do not have the "Most Annotated" start:Genes that do not have the "Most Annotated" start. Use the navigation hint to jump to your gene and note which of the three classification that it fall into. The next section of the Starterator report lists the called genes under each start number. This can be useful if there are only drafts in the pham or if your gene does not have the most recommended Starterator site. This can give you a feel of how represented the called start site is in the context of all genes in the pham. The final section lists the Gene Information, which the list of (start numbers, start positions). This is where you can go to translate the start numbers into their actual genome positions. The first line shows the start that was called, but most useful are the next lines that list all of the start locations and their corresponding Starterator start number. This is where you can correlate the start numbers with your possible translation start locations in the gene. Hope that this helps a little. Claire

Link to this post | posted 17 Apr, 2017 20:59
ClaireRinehart	Nick and Debbie, DNA master bases its z-scores on the raw scores of all possible open reading frames. PECAAN uses the open reading frames of candidates for all GeneMark and Glimmer called genes for the z-scores. Also, PECAAN uses double precision floating point calculations, which may cause slightly different results. Claire and Dex

Link to this post | posted 20 Mar, 2017 20:01

ClaireRinehart

Today I noted that there are 914 registered users of PECAAN and 230 phages in the PECAAN database. Since we have recently added a couple of new features that I have found especially useful in checking my student's annotations, I thought that I would highlight these in a post here just in case you had not discovered them yet. PECAAN now used both Aragorn and tRNA Scan SE to call tRNAs and tmRNAs. These pages are accessible through the top menu. By moving the vertical slider on the top sequence you can adjust the start and stop sites. Both Aragorn (red region) and tRNA Scan SE (blue region) calls are displayed on the top sequence map. Evidence and pictures of structures are shown for each method. An "tRNA Included" checkbox allows you to include (checked) or not include (unchecked) the tRNA. Edit and review logs for users are kept similar to the Genes log. Reports associated with tRNAs can be exported from the "Export" menu. The "Export CDS Full Annotation" report now includes the tRNAs and tmRNAs so that you do not need to edit the report before importing into DNA Master. A recent feature, that I am delighted with, is the "Pham Maps" page, which is available in the top menu. This page allows you to see a map of the latest edited genome features in a map of the Phams (yes, we use the standard pham colors). The map includes genes as colored boxes, if there is a pham number available, and tRNAs as + symbols. You can select one genome, from the cluster to which your working genome belongs, to compare to in a second line in the map. If you are displaying a gene and want to look at the map, clicking on the Pham Maps menu will take you to the map location containing the gene. Since I have multiple displays, I simply right click on the Pham Maps menu and either display the map in a separate tab or preferably in a separate window that I move to a separate monitor. I have found the Pham Map to be a super tools for reviewing student annotations because it is easy to see their gene calls and annotations in comparison to a published phage. I can see the pham number, start, stop and function for each gene I mouse over each gene in the map, so it is easy to comparatively check both the location and annotations from this one display. If you go to the Gene window and make changes for the "start" or "include" features and then go to the Pham Map the changes will be immediately reflected as it is refreshed. The great thing about Pham Maps is that you can change the Pham database phage that you are comparing your genome with! This allows you to compare different phages to your genome as you move along the genome during annotation and checking. Finally, we have made some changes in the User and Phages pages that are found under the Admin menu. These changes should make it easier to navigate through and edit within each of these pages. If you have questions or problems with PECAAN, Please email me at: claire.rinehart@wku.edu or call 270-745-6892 (M-F) 9-5 CT.