Blast And Fetching Data From Ncbi

Question: Blast And Fetching Data From Ncbi

8.1 years ago by

Hi, I am new to galaxy and I am wondering if it is possible to: 1) Fetch data from NCBI from the main galaxy portal? I assume this is possible from a local installation. For example, do a query say looking for a disease in rodents using Ratmine, export to Galaxy (did this fine) and then use the returned identifies to fetch sequence from NCBI. I can't seem to do this last bit - I don't even see NCBI under "Get Data". 2) Run blast from the main galaxy portal? Is this disabled due to too many users? Does this option appear once you have sequence? The context is our group at UAB is evaluating galaxy and I am just playing around to see what it can do. -John

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modified 8.1 years ago by Peter • 260 • written 8.1 years ago by John David Osborne • 160

8.1 years ago by

Peter • 260

Peter • 260 wrote:

I'd guess a wrapper for NCBI Entrez efetch could be written (if there isn't one already). I've written a BLAST+ wrapper which is now in galaxy-central, and will eventually be in galaxy-dist and thus potentially on the public Galaxy server (assuming it won't tax it too much). This doesn't (yet) offer the option to run the BLAST remotely at the NCBI (the wrapper could do this in theory). However, running a BLAST against the NCBI databases will cause difficulties for reproducibility (since we have no control over the databases, and the NCBI make regular updates). Would you be running your own Galaxy server? Peter

ADD COMMENT • link written 8.1 years ago by Peter • 260

8.1 years ago by

Peter • 260

Peter • 260 wrote:

Hi John, I've CC'd the mailing list again (assuming you omitted it by mistake - its easily done). Well, I'm sure they will consider it in future. But if I were in their shoes, I'd be a little nervous about the computational load it might impose. Within our institute we intend to offer BLAST running on our departmental server (in Galaxy) for Biologists to run large searches (e.g. multiple query sequences like a set of contigs) against both NCBI databases like NR and also in house ones (e.g. unpublished genomes), and as part of workflows (e.g. upload a FASTA file, blast against organism X, divide the FASTA file into those with good matches and those without). This is drifting into a discussion more suited for the galaxy dev mailing list though ;) Peter

ADD COMMENT • link written 8.1 years ago by Peter • 260

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