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Many molecular biologists are used to going to NCBI BLAST for quick, hassle-free BLAST searches of their genetic or protein sequences.

However, during the last American government shutdown in 2013, BLAST was rendered unusable due to lack of funding.

The incumbent president is also threatening to shutdown the government if funding for the Mexican border wall is not approved by the Democrats.

What are some alternatives for NCBI BLAST that are reasonably fast, easy to use, and would not be rendered unusable in the event of American government shutdowns? Ideally, the tools should encompass all of the standard BLAST sub-functions (pblast, PSI-blast, etc).

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b.nota is correct - Just further adding to his answer. The International Nucleotide Sequence Database Collaboration (INSDC) is a consortium between DNA Data-bank of Japan (DDBJ), EMBL-EBI and NCBI. Contributions to each of the 3 databases are shared on daily basis.

(Thanks to @KonradRudolph) Since EMBL-EBI is not directly accountable to any single government either financially or in terms of research directions so a (temporary) shutdown equivalent to that of the NCBI is vastly less likely. Rather, like CERN, it’s an international treaty organization and thus probably a lot more robust.

BLAST

Answering part 2 of your question: YES! BLAST is available in both DDBJ and EMBL-EBI on following links:

  1. BLAST - DDBJ
  2. NCBI BLAST+

Scope

Here is what INSDC's website says about its scope:

INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations.

Following table (taken from INSDC website) may help you have better understanding about respective data types comparison for 3 contributors:

INSDC Datatypes for its contributors

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    $\begingroup$ It’s worth noting that EMBL-EBI isn’t directly accountable to any one government either financially or in terms of research directions so a (temporary) shutdown equivalent to that of the NCBI is vastly less likely. Rather, like CERN, it’s an international treaty organisation and thus probably a lot more robust. $\endgroup$ – Konrad Rudolph Aug 25 '17 at 13:33
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BLAST can be localized to your machine. There are tutorials, such as Run-Blast-Local provided by NCBI. Note: you will need to download any/all databases you want to BLAST against locally. Other options for identifying ORFs and trying to identify potential genes include: USEARCH, VSEARCH (both claim to be as fast, or faster).

If you download entire databases, for example the nr db, running BLAST locally will be far slower than through a browser. I imagine creating customized, more specific databases would speed this up greatly (though I cannot confirm as I didn't get this far in my research).

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    $\begingroup$ While this is certainly a legitimate alternative, I don't imagine that a majority of molecular biologists (as opposed to bioinformaticians) have the requisite skill to install all of the packages on their own. $\endgroup$ – March Ho Aug 24 '17 at 23:18
  • $\begingroup$ @MarchHo Thank you for the helpful criticism. The link provides an brief how-to instruction to localize BLAST and includes a support email for any who require additional assistance. I should have included this information in the answer. I don't mean to claim this is by any means easy, you are indeed correct in putting forth that this method isn't without its challenges. Just providing additional solutions that I know of :) $\endgroup$ – jtth Aug 28 '17 at 14:28
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I think via Europe (EBI) will be an option, but I am not sure if it uses the American server or if its run on European servers.

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    $\begingroup$ Data is exchanged between both organisations which run their own servers. So the results should be the same. $\endgroup$ – Chris Aug 24 '17 at 13:40
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If the university also has the informatics department, they can setup BLAST server for the university no problem.

The server only needs to capture the input from the form and render the output as plain text, an easy task that can be implemented with the wide range of programming languages, server frameworks and operating systems, from Java to .NET, from Apache to node.js. Just restrict IPs for campus only to avoid abuse from the side.

Asking informaticians would eliminate the problem that may be difficult to run BLAST locally for each biologist separately. This can even be made an assignment for students, later putting the winner on the web.

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