Table 2 |
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|
Execution times of commonly used software: comparison of XplorSeq with command line implementation |
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|
Execution Time (sec.)1 |
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|
System A2 |
System B3 |
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|
Program |
XplorSeq4 |
Command Line |
XplorSeq4 |
Command Line |
Task |
Sequence Data |
|
|
||||||
|
phred |
50.5 (5.3)1 |
51.0 (2.9)1 |
23.3 (0.8)1 |
19.3 (0.5)1 |
Basecall |
768 .esd files. |
|
phrap |
167.0 (2.4) |
153.3 (0.8) |
30.5 (1.2) |
28.8 (1.5) |
Contig |
384 pairs of reads. |
|
blastall |
368.0 (2.4) |
345.3 (0.8) |
228.5 (1.2) |
221.3 (2.4) |
Local blast |
24 1585-mers |
|
XplorSeq |
69.0 (8.1) |
na |
21.2 (0.4) |
na |
Import fasta |
250,000 1585-mers |
|
XplorSeq |
130.8 (10.8) |
na |
12.2 (0.4) |
na |
Open XplorSeq file |
250,000 1585-mers |
|
XplorSeq |
160.8 (14.4) |
na |
11.7 (0.5) |
na |
Save XplorSeq file |
250,000 1585-mers |
|
XplorSeq |
60.5 (0.8) |
na |
46.3 (1.4) |
na |
Import fasta |
1,000,000 25-mers |
|
XplorSeq |
216.3 (11.2) |
na |
28.0 (0.6) |
na |
Open XplorSeq file |
1,000,000 25-mers |
|
XplorSeq |
34.3 (3.8) |
na |
16.5 (0.5) |
na |
Save XplorSeq file |
1,000,000 25-mers |
|
|
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|
1Elapsed time of execution: Mean (St. Dev) seconds. 2Executed on a 2 GHz Intel Core Duo MacBook Pro. 1 GB 667 MHz DDR2 SDRAM. Mac OSX version 10.5.4. 3Executed on a workstation with 2 × 3 GHz Quad-Core Intel Xeon processors. 8 GB 800 MHz DDR2 FB-DIMM. Mac OS X Server version 10.5.4 4Elapsed time includes export and import of data. |
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|
Frank BMC Bioinformatics 2008 9:420 doi:10.1186/1471-2105-9-420 |
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