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rdpstaff / RDPTools

Collection of commonly used RDP Tools for easy building
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Need to download the database #12

Open prakruthikr opened 8 years ago

prakruthikr commented 8 years ago

I am fetching below information from RDP Goto Hierarchy Browser>Search species> copy Strain type and Locus ID Example: S000413927 Bradyrhizobium oligotrophicum (T); JCM 1494; D78366
S000438365 Bradyrhizobium japonicum (T); USDA 6, 3I1b6, ATCC10324, SEMIA 5052, RCR 3425, ACCC 15032; original isolate received by USDA from Dr. K. Aso; U69638

Is there a way to fetch this information from the database directly by downloading the updated fasta/entire data base dump? Please guide me steps if any way available as I will be requiring this sort of data to download monthly basis? I downloaded bacteria aligned fasta file, but that does not serve the purpose

rdpstaffmsu commented 8 years ago

Dear User,

The direct data query is not current open to the public. You can download the entire dataset (aligned or unaligned) in batch using the links provided on RDP Resource page (http://rdp.cme.msu.edu/misc/resources.jsp). Let me know if it works for you.

Sincerely,

Benli Chai RDP Staff

On Tue, Jun 14, 2016 at 7:17 AM, prakruthikr notifications@github.com wrote:

I am fetching below information from RDP Goto Hierarchy Browser>Search species> copy Strain type and Locus ID Example: S000413927 Bradyrhizobium oligotrophicum (T); JCM 1494; D78366

S000438365 Bradyrhizobium japonicum (T); USDA 6, 3I1b6, ATCC10324, SEMIA 5052, RCR 3425, ACCC 15032; original isolate received by USDA from Dr. K. Aso; U69638

Is there a way to fetch this information from the database directly by downloading the updated fasta/entire data base dump? Please guide me steps if any way available as I will be requiring this sort of data to download monthly basis? I downloaded bacteria aligned fasta file, but that does not serve the purpose

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RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

koopkaup commented 6 years ago

Downloading unaligned bacterial and archaeal sequences (fasta format) is extremely slow and takes very long time. What could be the reason?