The search system has been retooled so that while the search is in progress, status messages are sent to the user in real time. This means that if the search is taking a long time, then every so often text will be presented to the user explaining what is happening. This makes a long search more palatable, and it also prevents the long searches from timing out and presenting the user with an internal server or proxy error. When the search is complete, the search results page will immediately pop up. For fast searches, the results come up so quickly that the status messages never show up. I have not tested this change thoroughly, but I hope to later today. The word search and the signature genes search should work if you want to see how the new system operates.
There have been three additions to the Signature Genes Tool.
- You can specify that only PEGs should be considered. This has become an issue because of all the new gene types that are appearing in NMPDR genomes.
- The scores are now between 0 and 1 instead of between 1 and 2. This makes them more intuitive in the case where the statistical algorithm is not being used.
- You can now discriminate using similarities instead of BBHs. This is a much slower process, but the new real-time status thing makes it less painful.
The NMPDR organism pages have every genome marked as new, which means the counts on the front page are almost certainly wrong. I will investigate this when I wake up this afternoon.
The Annotation button is still in place because there are still some fixes I need to make to the SEED Viewer support. The next thing I have on my list is fixing the BLAST search.
I have been told there are nine incorrect genomes in the NMPDR. As soon as they are fixed, I will reload, run the difference report, and begin the cutover and testing process. The next thing after the BLAST fixes are the drug target objects. Whether those get into v19 or v20 will depend on how long I have before the reload starts.