--- pir.html 2005/04/03 02:15:15 1.1 +++ pir.html 2005/04/06 22:40:40 1.4 @@ -3,52 +3,7 @@
You can download new data from the PIR ftp site and install the data directly. This is a two step process. First, we check to see whether the new file is more current than the old one (there is no point updating otherwise, unless, of course, you have added new genomes). Second, we actually get the data.-
Click on the button to see whether there are new updates. You will then see a page that looks something along these lines (of course, the times will be different!):+
Click on the button to see whether there are new updates. You will then see a page that looks something along these lines (of course, the times will be different!):
This example is for files that are all current.
Clicking on the "Update Data" or "Update Anyway" buttons will start the download and reinitiate the comparison of the SEED data with the PIR data. This starts a complete install of the PIR data which may take some time, so you will have to be patient! You can also use this to refresh or reinstall your data if you believe that the data is out of date (for example if you have added new genomes).+
Clicking on the "Update Data" or "Update Anyway" buttons will start the download and reinitiate the comparison of the SEED data with the PIR data. The downloading and installation of the data is run in the background using the script 'load_pirsf' because it takes a signficant amount of time and resources. You can monitor the progress in the SEED control panel. While the data is being installed you should really not use the PIR superfamilies. Although they will show up they are being edited, added, and deleted, and are therefore unstable. Installation of the data should take about 10-15 minutes.+ +
Once the update is run, you will see the front page again, however there will be a message telling you that the update is complete.+ -
Once the update is run, you will see the front page again, however there will be a message telling you that the update is complete+
The correspondence between PIR and SEED is highlighted in the spreadsheets. A sample of a few columns are shown below. Note this table is for demonstration purposes only and the correspondence will likely change. +
|Genome ID+||Organism+||Variant Code+||cysB+||cysC+||cysD+||cysI+||cysJ+||cysN+||cysQ+||cysS+|
|+||Yersinia pestis CO92 [B]+||+||2277+||3343 +||3345 +||3349+||3350 +||3344 +||3504+||3079 +|
|+||Vibrio parahaemolyticus RIMD 2210633 [B]+||+||1101+||296 +||292 +||2721+||2722 +||293 +||+||1150 +|
|+||Shigella flexneri 2a str. 301 [B]+||+||1222+||2595 +||2597 +||2601 +||2602 +||2596 +||4023+||444 +|
|+||Bacillus halodurans C-125 [B]+||+||+||1489 +||+||610 +||609 +||+||+||111, 112 [5, 3]+|
The columns of the table are colored based on the superfamilies that the proteins are in, and in theory each column should be the same color and complete throughout.
+Note that the small numbers that are slightly superscripted  are linked to the PIR correspondence table so you can click through and see proteins missing from either side as described above.
This example demonstrates this different aspects of the PIR/SEED interactions:+