Benchmark tests of NCBI Blast+ Remote
NCBI BLAST+ has -remote option and BLAST+ searches can be performed in NCBI facility with this option.
We performed the benchmark tests of NCBI Blast+ 2.2.24 with -remote option and compared it with local NCBI Blast+ 2.2.24 results.
 

Up-to-date as of 12/4/2010

 
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1. Test Conditions
OS: Mac OS X 10.6.5 Snow Leopard
Hardware: iMac, Core 2 Duo@3.06GHz, 8GB Memory
32 bit NCBI Blast+: 2.2.24 downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.24/ncbi-blast-2.2.24+-universal-macosx.tar.gz
64 bit NCBI Blast+: 2.2.24 built by us.  64 bit binaries are available here
Number of threads are 2 for both of 32 bit and 64 bit NCBI BLAST+.
Numbers in the table below are real of /usr/bin/time in seconds except "NCBI Blast+ at NCBI Web Site".
2. Results
traditional blastn
DB: env_nt.00 - env_nt.02 combined downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ 
18,402,403 sequences; 7,566,542,886 total letters
Query Sequence: AF287139, 606 letters
NCBI Blast+ Remote1) Local 64 bit NCBI Blast+2) Local 32 bit NCBI Blast+ NCBI Blast+ at NCBI Web Site3)
29.2 13.1 14.9 12
blastp
DB: env_nr.00 - env_nr.01 combined downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/
6,031,295 sequences; 1,208,072,170 total letters
Query Sequence: ACL81455, 301 letters
NCBI Blast+ Remote1) Local 64 bit NCBI Blast+2) Local 32 bit NCBI Blast+ NCBI Blast+ at NCBI Web Site3)
40.7 17.2 20.2 24
         
3. Conclusions
3.1.traditional blastn
      Local 64 bit NCBI Blast+ and NCBI Blast+ at NCBI Web Site are the fastest.
      NCBI Blast+ Remote is the slowest.
3.2.blastp
      Local 64 bit NCBI Blast+ is the fastest.
      NCBI Blast+ Remote is the slowest.
If your Mac have processors faster than Core 2 Duo and more than 8GB memory, local 64 bit NCBI Blast+ search will be performed fast enough against any database.  Free trial of BlastStation-Local64, which has built-in 64 bit NCBI Blast+ 2.2.24, is available here.
1) BLAST searches were performed every 30 minutes for 24 hours.  The number shown in the table is the average elapsed time.
2) NCBI Blast+ was built with --with-64 configuration option.  Please refer to How to Build NCBI Blast+ for Mac OS X for details to build.  This 64 bit binary is available for download here .  It should work on Mac OS X 10.6 and 10.5 with 64 bit Intel processors, such as Core 2 Duo and Xeon.
3) BLAST searches were performed several times on the weekend and shortest elapsed time is shown in the table.  Elapsed time is measured from the time Submit button is clicked until the Search Summary page is rendered.
 
 

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