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Question: bacterial complete nt database to apply blastn
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gravatar for gm
8 months ago by
gm • 0
gm • 0 wrote:

Hi all,

the present question has been many times addressed but I failed to find any definitive and satisfying answer.

I'm trying to run blustn from Galaxy. I'm interested in finding bacterial contaminants within my contigs.

Which is the most effective and easier way to create such a complete db? I suppose makeblastdb should work fine,

but if it is the case, where can I download data for all bacteria? And then, should I need to download assemblies or

nucleotides?

And where to find complete database to use with blastp?

Thanks a lot for any hint you will provide
reference blast database blastn galaxy • 383 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by gm • 0
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Use the tools under the group NCBI BLAST+ with a BLAST or fasta dataset from the history. See the tool form's help for more details about these choices, example: NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) (Galaxy Version 0.2.01)

If this is your own server, indexes can be set up on the server to be "built-in".

The NCBI BLAST+ repository help in the ToolShed explains where some NCBI sources for pre-indexed BLAST databases are, plus you can check directly at NCBI directly for what each division contains and where to find them for download (upload to Galaxy after, using FTP). Or, you can index any fasta into a BLAST database if not already pre-computed.

Databases at NCBI:

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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