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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 |
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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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