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: or call 270-745-6892 (M-F) 9-5 CT.