Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign88 - back to list
Summary
./analyse_probe_search_results : Tue Dec 20 11:37:44 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign88 assembly : NCBIM34 bias : 5prime chromosome : 11 id : 79 strand : 1 ------------- Design window length: 3501bp All jobs for probe design are successful - total: 56 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 1114 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 : 1114/1114 Putative probes that are unique : 0/1114 No putative probes pass with the above criteria Now trying: score-ratio 2, and percent repetitive 40 Putative probes exceeding selection criteria : 58/1114 (both unique and not unique) Putative probes with successfully-picked primers: 52/58 Identified 3 '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/probedesign88.png)
Unique putative probes
No probes
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
75877 | 500 | 14.9 | 2500 | 20.2 | 1375 | -25.5 |
75878 | 500 | 14.9 | 2500 | 20.2 | 1400 | -25.5 |
75879 | 500 | 14.2 | 2500 | 20.2 | 1425 | -26.2 |
75880 | 500 | 10.7 | 2500 | 20.2 | 1450 | -29.7 |
75881 | 500 | 8.6 | 2500 | 20.6 | 1475 | -32.6 |
75876 | 500 | 14.9 | 2500 | 24.6 | 1350 | -34.3 |
75761 | 550 | 16.4 | 2750 | 27.5 | 1323 | -38.5 |
75762 | 550 | 16.4 | 2750 | 27.5 | 1350 | -38.5 |
75763 | 550 | 15.6 | 2750 | 27.5 | 1377 | -39.3 |
75767 | 550 | 7.6 | 2750 | 24.4 | 1485 | -41.1 |
75764 | 550 | 10.9 | 2750 | 27.5 | 1404 | -44.0 |
75882 | 500 | 7.1 | 2500 | 25.6 | 1500 | -44.1 |
75875 | 500 | 14.9 | 2500 | 29.6 | 1325 | -44.3 |
75664 | 600 | 8.3 | 3000 | 26.7 | 1470 | -45.0 |
75765 | 550 | 9.4 | 2750 | 27.5 | 1431 | -45.6 |
75766 | 550 | 7.7 | 2750 | 27.1 | 1458 | -46.5 |
75768 | 550 | 7.6 | 2750 | 27.1 | 1512 | -46.6 |
75883 | 500 | 6.9 | 2500 | 26.8 | 1525 | -46.7 |
75663 | 600 | 8.3 | 3000 | 27.8 | 1440 | -47.4 |
75884 | 500 | 6.9 | 2500 | 27.4 | 1550 | -47.9 |
75760 | 550 | 16.4 | 2750 | 32.2 | 1296 | -48.0 |
75658 | 600 | 17.9 | 3000 | 33.5 | 1290 | -49.1 |
75659 | 600 | 17.0 | 3000 | 33.5 | 1320 | -50.0 |
75657 | 600 | 17.9 | 3000 | 35.5 | 1260 | -53.1 |
75665 | 600 | 8.3 | 3000 | 31.2 | 1500 | -54.0 |
75660 | 600 | 12.9 | 3000 | 33.5 | 1350 | -54.1 |
75874 | 500 | 14.9 | 2500 | 34.6 | 1300 | -54.3 |
75569 | 650 | 9.0 | 3250 | 32.3 | 1408 | -55.6 |
75570 | 650 | 9.0 | 3250 | 32.3 | 1440 | -55.6 |
75571 | 650 | 9.0 | 3250 | 32.3 | 1472 | -55.6 |
75486 | 700 | 9.7 | 3500 | 32.7 | 1470 | -55.8 |
75769 | 550 | 7.6 | 2750 | 32.0 | 1539 | -56.4 |
75661 | 600 | 10.3 | 3000 | 33.5 | 1380 | -56.7 |
75572 | 650 | 9.0 | 3250 | 33.1 | 1504 | -57.2 |
75662 | 600 | 8.3 | 3000 | 32.8 | 1410 | -57.3 |
75759 | 550 | 16.4 | 2750 | 37.1 | 1269 | -57.8 |
75564 | 650 | 19.3 | 3250 | 38.6 | 1248 | -57.9 |
75885 | 500 | 6.9 | 2500 | 32.4 | 1575 | -57.9 |
75565 | 650 | 18.5 | 3250 | 38.6 | 1280 | -58.8 |
75563 | 650 | 19.3 | 3250 | 39.5 | 1216 | -59.7 |
75568 | 650 | 9.0 | 3250 | 35.5 | 1376 | -62.1 |
75485 | 700 | 9.7 | 3500 | 36.1 | 1435 | -62.6 |
75666 | 600 | 8.3 | 3000 | 35.8 | 1530 | -63.4 |
75667 | 600 | 8.3 | 3000 | 36.0 | 1560 | -63.7 |
75408 | 750 | 10.4 | 3750 | 37.2 | 1443 | -64.0 |
75483 | 700 | 9.7 | 3500 | 37.1 | 1365 | -64.6 |
75484 | 700 | 9.7 | 3500 | 37.1 | 1400 | -64.6 |
75407 | 750 | 10.4 | 3750 | 37.6 | 1406 | -64.8 |
75487 | 700 | 9.7 | 3500 | 37.3 | 1505 | -64.9 |
75566 | 650 | 12.2 | 3250 | 38.6 | 1312 | -65.0 |
75409 | 750 | 10.4 | 3750 | 38.1 | 1480 | -65.9 |
75770 | 550 | 7.6 | 2750 | 36.9 | 1566 | -66.2 |
75567 | 650 | 9.5 | 3250 | 38.6 | 1344 | -67.8 |
75886 | 500 | 6.9 | 2500 | 37.4 | 1600 | -67.9 |
75482 | 700 | 9.7 | 3500 | 39.6 | 1330 | -69.5 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
75873 | 500 | 14.9 | 2500 | 39.6 | 1275 | -64.3 |
75573 | 650 | 9.0 | 3250 | 37.2 | 1536 | -65.5 |
75771 | 550 | 7.6 | 2750 | 39.1 | 1593 | -70.6 |
Overall score = score_ratio - 2 * repetitive DNA content