Table 2

Execution times of commonly used software: comparison of XplorSeq with command line implementation

Execution Time (sec.)1

System A2

System B3

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


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.

Frank BMC Bioinformatics 2008 9:420   doi:10.1186/1471-2105-9-420

Open Data