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Table 2 Pipeline run time for different probe design sets

From: Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays

Genomes

Cand. C. ruddii PV

B. garinii Pbi

P. gingivalis W83

E. coli K12 MG1655

S. cellulosum'So ce 56'

Genome size

~0.16 Mbp

~1.22 Mbp

~2.34 Mbp

~4.6 Mbp

~13 Mbp

Characteristic

Small

Multiple

Oral pathogen

E. coli

Large

Probe number (NG format)

72 K (4*72 K)

192.5 K (385 K/2)

385 K

770 K (2*385 K)

1620 K (12*135 K)

Probe size

50

50

50

50

50

Min. probe size

45

45

45

45

48

Run time

     

   Step 1

<1 min

<2 min

2 min

6 min

16 min

   Step 2

<1 min

8 min

16 min

31 min

1 h 3 min

   Step 3 (blastn, -W 7)*

12 min

1 h 43 min

2 h 57 min

6 h 37 min

76 h

   Step 4 (hybrid-ss-min)*

6 min

43 min

69 min

2 h 25 min

8 h

   Step 5,6

<1 min

7 min

6 min

11 min

31 min

Total run time

~15 min

~2 h

~3 h 21 min

~7 h 25 min

~77 h 50 min

  1. *Run in parallel, only most time consuming step is included in the total run time. Word size 7 is used for blastn.