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.
Comments (1)
Hi Bruce,
the next nmpdr has lost the count of number of results returned, which I liked very much. This applies to all search results, not just sig genes.
I am again feeling like I am not entirely sane because the comparisons I made with sig genes yesterday are now giving me something different today. The RNAs have disappeared from the output on the live site, so that makes the just pegs button on the next version redundant. If the tool was doing what I thought it was, the check box shouldn't be required as the only possible output is pegs in the first place. I began to revise the instructions for that page, but now I am hung up on the check boxes. It already just shows pegs, so that check box is confusing; and the use statistical al gore next to use similiarities is also not explained. Does the algorithm need to be a choice? It automatically uses the commonality factor for compare al gore for contrast anyway, right?
have a weekend, leslie
Posted by leslie | March 30, 2007 4:18 PM
Posted on March 30, 2007 16:18