Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign76 - back to list
Summary
./analyse_probe_search_results : Tue Oct 18 14:43:59 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign76 assembly : NCBIM34 bias : 5prime chromosome : X id : 61 strand : 1 ------------- Design window length: 2001bp All jobs for probe design are successful - total: 25 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 494 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 : 494/494 Putative probes that are unique : 47/494 Putative probes exceeding selection criteria : 2/494 (but not unique) Putative probes with successfully-picked primers: 49/49 Identified 1 '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/probedesign76.png)
Unique putative probes
Putative probe ID | Length | Actual | %rep DNA | Distance |
---|---|---|---|---|
59460 | 800 | 4000 | - | 0 |
59491 | 750 | 3750 | - | 0 |
59492 | 750 | 3750 | - | 37 |
59525 | 700 | 3500 | - | 0 |
59526 | 700 | 3500 | - | 35 |
59527 | 700 | 3500 | - | 70 |
59528 | 700 | 3500 | - | 105 |
59563 | 650 | 3250 | - | 0 |
59564 | 650 | 3250 | - | 32 |
59565 | 650 | 3250 | - | 64 |
59566 | 650 | 3250 | - | 96 |
59567 | 650 | 3250 | - | 128 |
59606 | 600 | 3000 | - | 0 |
59607 | 600 | 3000 | - | 30 |
59608 | 600 | 3000 | - | 60 |
59609 | 600 | 3000 | - | 90 |
59610 | 600 | 3000 | - | 120 |
59611 | 600 | 3000 | - | 150 |
59612 | 600 | 3000 | - | 180 |
59653 | 550 | 2750 | - | 0 |
59654 | 550 | 2750 | - | 27 |
59655 | 550 | 2750 | - | 54 |
59656 | 550 | 2750 | - | 81 |
59657 | 550 | 2750 | - | 108 |
59658 | 550 | 2750 | - | 135 |
59659 | 550 | 2750 | - | 162 |
59660 | 550 | 2750 | - | 189 |
59661 | 550 | 2750 | - | 216 |
59662 | 550 | 2750 | - | 243 |
59707 | 500 | 2500 | - | 0 |
59708 | 500 | 2500 | - | 25 |
59709 | 500 | 2500 | - | 50 |
59710 | 500 | 2500 | - | 75 |
59711 | 500 | 2500 | - | 100 |
59712 | 500 | 2500 | - | 125 |
59713 | 500 | 2500 | - | 150 |
59714 | 500 | 2500 | - | 175 |
59715 | 500 | 2500 | - | 200 |
59716 | 500 | 2500 | - | 225 |
59717 | 500 | 2500 | - | 250 |
59718 | 500 | 2500 | - | 275 |
59719 | 500 | 2500 | - | 300 |
59568 | 650 | 3250 | 0.8 | 160 |
59613 | 600 | 3000 | 0.8 | 210 |
59493 | 750 | 3750 | 2.5 | 74 |
59663 | 550 | 2750 | 2.7 | 270 |
59720 | 500 | 2500 | 4.0 | 325 |
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
59461 | 800 | 21.4 | 4000 | 4.4 | 40 | 12.6 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
59529 | 700 | 18.7 | 3500 | 5.0 | 140 | 8.7 |
Overall score = score_ratio - 2 * repetitive DNA content