Skip to main content

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.