Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign92 - back to list
Summary
./analyse_probe_search_results : Wed Dec 21 12:00:21 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign92 assembly : NCBIM34 bias : 5prime chromosome : 18 id : 83 strand : 1 ------------- Design window length: 2668bp All jobs for probe design are successful - total: 39 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 768 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 : 768/768 Putative probes that are unique : 0/768 Putative probes exceeding selection criteria : 69/768 (both unique and not unique) Putative probes with successfully-picked primers: 58/69 Identified 4 '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/probedesign92.png)
Unique putative probes
No probes
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
78464 | 850 | 25.9 | 4250 | 0.2 | 588 | 25.4 |
78509 | 800 | 24.4 | 4000 | - | 600 | 24.4 |
78510 | 800 | 24.4 | 4000 | 0.5 | 640 | 23.4 |
78557 | 750 | 22.9 | 3750 | - | 592 | 22.9 |
78558 | 750 | 22.9 | 3750 | - | 629 | 22.9 |
78559 | 750 | 22.9 | 3750 | - | 666 | 22.9 |
78508 | 800 | 24.4 | 4000 | 0.9 | 560 | 22.6 |
78610 | 700 | 21.3 | 3500 | - | 595 | 21.3 |
78611 | 700 | 21.3 | 3500 | - | 630 | 21.3 |
78612 | 700 | 21.3 | 3500 | - | 665 | 21.3 |
78613 | 700 | 21.3 | 3500 | - | 700 | 21.3 |
78614 | 700 | 21.3 | 3500 | - | 735 | 21.3 |
78463 | 850 | 25.9 | 4250 | 2.5 | 546 | 21.0 |
78422 | 900 | 27.4 | 4500 | 3.4 | 540 | 20.6 |
78668 | 650 | 19.8 | 3250 | - | 576 | 19.8 |
78669 | 650 | 19.8 | 3250 | - | 608 | 19.8 |
78670 | 650 | 19.8 | 3250 | - | 640 | 19.8 |
78671 | 650 | 19.8 | 3250 | - | 672 | 19.8 |
78672 | 650 | 19.8 | 3250 | - | 704 | 19.8 |
78673 | 650 | 19.8 | 3250 | - | 736 | 19.8 |
78674 | 650 | 19.8 | 3250 | - | 768 | 19.8 |
78556 | 750 | 22.9 | 3750 | 1.6 | 555 | 19.7 |
78609 | 700 | 21.3 | 3500 | 1.0 | 560 | 19.3 |
78560 | 750 | 22.9 | 3750 | 2.3 | 703 | 18.3 |
78733 | 600 | 18.3 | 3000 | - | 570 | 18.3 |
78734 | 600 | 18.3 | 3000 | - | 600 | 18.3 |
78735 | 600 | 18.3 | 3000 | - | 630 | 18.3 |
78736 | 600 | 18.3 | 3000 | - | 660 | 18.3 |
78737 | 600 | 18.3 | 3000 | - | 690 | 18.3 |
78738 | 600 | 18.3 | 3000 | - | 720 | 18.3 |
78739 | 600 | 18.3 | 3000 | - | 750 | 18.3 |
78740 | 600 | 18.3 | 3000 | - | 780 | 18.3 |
78741 | 600 | 18.3 | 3000 | - | 810 | 18.3 |
78804 | 550 | 18.0 | 2750 | - | 567 | 18.0 |
78805 | 550 | 18.0 | 2750 | - | 594 | 18.0 |
78742 | 600 | 18.3 | 3000 | 0.7 | 840 | 17.0 |
78806 | 550 | 16.8 | 2750 | - | 621 | 16.8 |
78807 | 550 | 16.8 | 2750 | - | 648 | 16.8 |
78808 | 550 | 16.8 | 2750 | - | 675 | 16.8 |
78809 | 550 | 16.8 | 2750 | - | 702 | 16.8 |
78810 | 550 | 16.8 | 2750 | - | 729 | 16.8 |
78811 | 550 | 16.8 | 2750 | - | 756 | 16.8 |
78812 | 550 | 16.8 | 2750 | - | 783 | 16.8 |
78813 | 550 | 16.8 | 2750 | - | 810 | 16.8 |
78814 | 550 | 16.8 | 2750 | - | 837 | 16.8 |
78815 | 550 | 16.8 | 2750 | - | 864 | 16.8 |
78887 | 500 | 16.7 | 2500 | - | 625 | 16.7 |
78888 | 500 | 16.7 | 2500 | - | 650 | 16.7 |
78885 | 500 | 16.3 | 2500 | - | 575 | 16.3 |
78886 | 500 | 16.3 | 2500 | - | 600 | 16.3 |
78675 | 650 | 19.8 | 3250 | 2.2 | 800 | 15.5 |
78889 | 500 | 15.2 | 2500 | - | 675 | 15.2 |
78890 | 500 | 15.2 | 2500 | - | 700 | 15.2 |
78891 | 500 | 15.2 | 2500 | - | 725 | 15.2 |
78892 | 500 | 15.2 | 2500 | - | 750 | 15.2 |
78893 | 500 | 15.2 | 2500 | - | 775 | 15.2 |
78894 | 500 | 15.2 | 2500 | - | 800 | 15.2 |
78895 | 500 | 15.2 | 2500 | - | 825 | 15.2 |
78896 | 500 | 15.2 | 2500 | - | 850 | 15.2 |
78897 | 500 | 15.2 | 2500 | - | 875 | 15.2 |
78898 | 500 | 15.2 | 2500 | - | 900 | 15.2 |
78899 | 500 | 15.2 | 2500 | - | 925 | 15.2 |
78816 | 550 | 16.8 | 2750 | 0.9 | 891 | 15.0 |
78884 | 500 | 16.3 | 2500 | 3.4 | 550 | 9.5 |
78615 | 700 | 16.9 | 3500 | 4.9 | 770 | 7.2 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
78667 | 650 | 19.8 | 3250 | 3.5 | 544 | 12.7 |
78732 | 600 | 19.6 | 3000 | 4.5 | 540 | 10.6 |
78900 | 500 | 15.2 | 2500 | 2.8 | 950 | 9.6 |
78803 | 550 | 18.0 | 2750 | 4.9 | 540 | 8.2 |
Overall score = score_ratio - 2 * repetitive DNA content