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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 2.2.24 downloaded from
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.24/ncbi-blast-2.2.24+-win32.exe
64-bit 2.2.24 downloaded from
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.24/ncbi-blast-2.2.24+-win64.exe
NCBI Blast: 32-bit 2.2.24 downloaded from
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.24/blast-2.2.24-ia32-win32.exe
64-bit 2.2.24 downloaded from
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.24/blast-2.2.24-x64-win64.exe
Numbers in the table below are in seconds. |
|
| 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 |
|
# of Threads1) |
32-bit NCBI Blast+ |
64-bit NCBI Blast+ |
32-bit NCBI Blast |
64-bit NCBI Blast |
|
1 |
29.5 |
22.7 |
54.1 |
21.3 |
|
2 |
15.3 |
15.1 |
34.7 |
11.5 |
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 |
|
# of Threads1) |
32-bit NCBI Blast+ |
64-bit NCBI Blast+ |
32-bit NCBI Blast |
64-bit NCBI Blast |
|
1 |
30.5 |
27.1 |
31.2 |
25.4 |
|
2 |
16.7 |
17.2 |
18.5 |
14.5 |
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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, but
almost same speed as 32-bit NCBI Blast+. |
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| 1) Specified -num_threads
n in the command arguments. |
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