Hi Chris, The sim service provides access to a precomputed all-to-all blast search, so I don't think it will help for the query you need. I've been exploring/testing the idea of using blast for the Translation service, to be able to map sequences or gene calls to features of a specific genome. I can say that blast is installed on the kbase images (including tblastn), so it is easy to call from a kbase service, but it is not yet wrapped as a general kbase service as far as I know. That said, you could take a look at the blast_tester.pl in the Translation repo or the implementation of the map_to_fid method of the Translation service for an example of how I'm calling blastp and creating a blast database for a specific genome. let me know if you have questions on this. -michael On Fri, Jan 4, 2013 at 5:41 AM, Thomas Brettin <[email protected]> wrote:
Have you checked out the sim service Bob stood up?
On Jan 3, 2013, at 10:10 PM, Christopher Henry <[email protected]> wrote:
So I'm wondering what kinds of blast services exist for KBase at the moment.
Do we offer services that enable a user to blast a particular sequence against all genomes in our database?
Specifically, I'm interested in a service that lets me "TBlastN" a series of candidate protein sequences against a specified set of KBase genomes. The idea is I think these proteins might be in these genomes, but they're not being spotted in part because of an error or omission in the gene calls.
Do we have something that does this? If not, it seems like a good service to create. Seems like KBase should support all forms of blast if possible. If it's missing and we think we want to create it, is there an existing service in KBase that this would fit nicely into? Perhaps the genome annotation service?
Chris _______________________________________________ Kbase-devel mailing list [email protected] https://lists.kbase.us/mailman/listinfo/kbase-devel
Thomas Brettin 865-603-7760 (cell) [email protected]
_______________________________________________ Kbase-devel mailing list [email protected] https://lists.kbase.us/mailman/listinfo/kbase-devel