Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign9 - back to list
Summary
./analyse_probe_search_results : Tue Mar 13 19:10:57 2007
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign9 assembly : NCBIM36 bias : 5prime chromosome : 2 id : 15 strand : 1 ------------- Design window length: 2893bp All jobs for probe design are successful - total: 22 Fetched conf : Exonerate mouse_NCBIM36 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted Fetched 434 putative probes to analyse Selection criteria to rank probes: Minimum score ratio : 10 (i.e. self-hit must score at least 10 times higher than the next best hit) Maximum percent repetitive bases: 5 Favour probes to the 5prime end of design window ------------------------ Putative probes without hits : 0 Putative probes with single_self_hit : 434/434 Putative probes that are unique : 46/434 Putative probes exceeding selection criteria : 52/434 (both unique and not unique) Putative probes with successfully-picked primers: 52/52 Identified 0 'redundant' probes exceeding selection criteria (but wholly contained by other probes, and higher repetitive DNA content)
Image
Unique (yellow), passed (green) and failed putative probes in the design window
![Chart](gfx/probedesign9.png)
Unique putative probes
Putative probe ID | Length | Actual | %rep DNA | Distance |
---|---|---|---|---|
22684 | 700 | 3500 | - | 0 |
22716 | 650 | 3250 | - | 0 |
22717 | 650 | 3250 | - | 65 |
22751 | 600 | 3000 | - | 0 |
22752 | 600 | 3000 | - | 60 |
22753 | 600 | 3000 | - | 120 |
22790 | 550 | 2750 | - | 0 |
22791 | 550 | 2750 | - | 55 |
22792 | 550 | 2750 | - | 110 |
22793 | 550 | 2750 | - | 165 |
22833 | 500 | 2500 | - | 0 |
22834 | 500 | 2500 | - | 50 |
22835 | 500 | 2500 | - | 100 |
22836 | 500 | 2500 | - | 150 |
22837 | 500 | 2500 | - | 200 |
22874 | 500 | 2500 | 0.8 | 2050 |
22642 | 800 | 4000 | 15.2 | 1120 |
22670 | 750 | 3750 | 16.3 | 1125 |
22700 | 700 | 3500 | 17.4 | 1120 |
22701 | 700 | 3500 | 17.4 | 1190 |
22616 | 850 | 4250 | 17.6 | 1105 |
22733 | 650 | 3250 | 18.8 | 1105 |
22734 | 650 | 3250 | 18.8 | 1170 |
22735 | 650 | 3250 | 18.8 | 1235 |
22671 | 750 | 3750 | 19.3 | 1200 |
22769 | 600 | 3000 | 20.3 | 1080 |
22770 | 600 | 3000 | 20.3 | 1140 |
22771 | 600 | 3000 | 20.3 | 1200 |
22772 | 600 | 3000 | 20.3 | 1260 |
22773 | 600 | 3000 | 20.3 | 1320 |
22855 | 500 | 2500 | 22.0 | 1100 |
22702 | 700 | 3500 | 22.1 | 1260 |
22810 | 550 | 2750 | 22.2 | 1100 |
22811 | 550 | 2750 | 22.2 | 1155 |
22812 | 550 | 2750 | 22.2 | 1210 |
22813 | 550 | 2750 | 22.2 | 1265 |
22814 | 550 | 2750 | 22.2 | 1320 |
22815 | 550 | 2750 | 22.2 | 1375 |
22736 | 650 | 3250 | 22.3 | 1300 |
22856 | 500 | 2500 | 24.4 | 1150 |
22857 | 500 | 2500 | 24.4 | 1200 |
22858 | 500 | 2500 | 24.4 | 1250 |
22859 | 500 | 2500 | 24.4 | 1300 |
22860 | 500 | 2500 | 24.4 | 1350 |
22861 | 500 | 2500 | 24.4 | 1400 |
22862 | 500 | 2500 | 29.0 | 1450 |
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
22655 | 750 | 17.6 | 3750 | - | 0 | 17.6 |
22685 | 700 | 12.2 | 3500 | - | 70 | 12.2 |
22838 | 500 | 11.7 | 2500 | - | 250 | 11.7 |
22718 | 650 | 11.3 | 3250 | - | 130 | 11.3 |
22754 | 600 | 10.4 | 3000 | - | 180 | 10.4 |
22628 | 800 | 12.3 | 4000 | 1.6 | 0 | 9.1 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
No probes
Overall score = score_ratio - 2 * repetitive DNA content