Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign32 - back to list
Summary
./analyse_probe_search_results : Mon Sep 5 11:27:03 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign32 assembly : NCBIM34 bias : 5prime chromosome : X id : 7 strand : 1 ------------- Design window length: 2432bp All jobs for probe design are successful - total: 27 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 537 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 : 537/537 No putative probes pass with the above criteria Using: score-ratio 2, and percent repetitive 40 Putative probes exceeding selection criteria: 34/537 PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW --------------------------------------------------------------
Image
Unique (yellow), passed (green) and failed putative probes in the design window
Unique putative probes
No probes
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
6567 | 500 | 10.9 | 2500 | 25.2 | 825 | -39.5 |
6566 | 500 | 9.1 | 2500 | 25.2 | 800 | -41.3 |
6568 | 500 | 7.8 | 2500 | 25.2 | 850 | -42.6 |
6569 | 500 | 5.8 | 2500 | 25.2 | 875 | -44.6 |
6570 | 500 | 4.7 | 2500 | 25.2 | 900 | -45.7 |
6565 | 500 | 6.4 | 2500 | 30.0 | 775 | -53.6 |
6571 | 500 | 3.9 | 2500 | 29.6 | 925 | -55.3 |
6493 | 550 | 8.6 | 2750 | 32.0 | 783 | -55.4 |
6564 | 500 | 5.7 | 2500 | 30.6 | 750 | -55.5 |
6494 | 550 | 7.6 | 2750 | 32.0 | 810 | -56.4 |
6492 | 550 | 6.4 | 2750 | 32.0 | 756 | -57.6 |
6495 | 550 | 5.7 | 2750 | 32.0 | 837 | -58.3 |
6496 | 550 | 4.7 | 2750 | 32.0 | 864 | -59.3 |
6497 | 550 | 3.8 | 2750 | 32.0 | 891 | -60.2 |
6491 | 550 | 5.8 | 2750 | 35.6 | 729 | -65.4 |
6563 | 500 | 5.3 | 2500 | 35.6 | 725 | -65.9 |
6572 | 500 | 3.3 | 2500 | 34.6 | 950 | -65.9 |
6498 | 550 | 3.3 | 2750 | 34.7 | 918 | -66.2 |
6110 | 950 | 7.6 | 4750 | 37.6 | 282 | -67.5 |
6081 | 1000 | 8.0 | 5000 | 38.0 | 300 | -68.0 |
6490 | 550 | 5.2 | 2750 | 36.7 | 702 | -68.2 |
6427 | 600 | 6.8 | 3000 | 37.7 | 750 | -68.5 |
6428 | 600 | 6.7 | 3000 | 37.7 | 780 | -68.6 |
6080 | 1000 | 8.0 | 5000 | 38.5 | 250 | -69.0 |
6426 | 600 | 6.1 | 3000 | 37.7 | 720 | -69.2 |
6429 | 600 | 5.3 | 3000 | 37.7 | 810 | -70.1 |
6430 | 600 | 4.2 | 3000 | 37.7 | 840 | -71.2 |
6431 | 600 | 3.5 | 3000 | 37.7 | 870 | -71.8 |
6432 | 600 | 3.0 | 3000 | 37.7 | 900 | -72.3 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
6143 | 900 | 7.2 | 4500 | 39.7 | 315 | -72.1 |
6111 | 950 | 7.6 | 4750 | 39.9 | 329 | -72.2 |
6425 | 600 | 5.6 | 3000 | 39.2 | 690 | -72.7 |
6573 | 500 | 2.9 | 2500 | 39.6 | 975 | -76.3 |
6499 | 550 | 2.8 | 2750 | 39.6 | 945 | -76.5 |
Overall score = score_ratio - 2 * repetitive DNA content