Benchmark tests of NCBI Blast+ on Windows
We performed the benchmark tests of NCBI Blast+ 2.2.26 and compared it with NCBI Blast 2.2.26 results.
 
Up-to-date as of 7/18/2012
 
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1. Test Conditions
OS: 64-bit Windows 7 on Parallels Desktop 5
Hardware: iMac, Core 2 Duo@3.06GHz, 4GB Memory
NCBI Blast+: 32-bit 2.2.26 downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-win32.exe
64-bit 2.2.26 downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-win64.exe
NCBI Blast: 32-bit 2.2.26 downloaded from
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/blast-2.2.26-ia32-win32.exe
64-bit 2.2.26 downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/blast-2.2.26-x64-win64.exe
Numbers in the table below are in seconds.
2. Results
traditional blastn
DB: env_nt.00 - env_nt.03 combined downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ 
18,485,111 sequences; 7,649,819,738 total letters
Query Sequence: AF287139, 606 letters

Numbers in parentheses are results by NCBI Blast+ 2.2.24 or NCBI Blast 2.2.24 against env_nt (18,402,403 sequences; 7,566,542,886 total letters)
# of Threads1) 32-bit NCBI Blast+ 64-bit NCBI Blast+ 32-bit NCBI Blast 64-bit NCBI Blast
1 29.4(29.5) 24.2(22.7) 78.0(54.1) 19.6(21.3)
2 15.9(15.3) 13.5(15.1) 46.9(34.7) 12.0(11.5)
blastp
DB: env_nr.00 - env_nr.01 combined downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/
6,050,066 sequences; 1,213,377,474 total letters
Query Sequence: ACL81455, 301 letters
Numbers in parentheses are results by NCBI Blast+ 2.2.24 or NCBI Blast 2.2.24 against env_nr (6,031,295 sequences; 1,208,072,170 total letters)
# of Threads1) 32-bit NCBI Blast+ 64-bit NCBI Blast+ 32-bit NCBI Blast 64-bit NCBI Blast
1 32.4(30.5) 28.0(27.1) 25.5(31.2) 22.6(25.4)
2 17.0(16.7) 15.8(17.2) 14.5(18.5) 12.6(14.5)
         
3. Conclusions
3.1.blastn
      64-bit NCBI Blast is the fastest for all numbers of threads.
      32-bit NCBI Blast is the slowest.
3.2.blastp
      64-bit NCBI Blast is the fastest for all numbers of threads.
      32-bit NCBI Blast+ is the slowest.

64-bit NCBI Blast is used in BlastStation-Local64 for Windows because of these results.  On the other hand, 64-bit NCBI Blast+ is used in BlastStation-Local64 for Mac OS X.   Benchmark results on Mac OS X are completely different.

1) Specified -num_threads n in the command arguments.
 
 
 
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