Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign52 - back to list
Summary
./analyse_probe_search_results : Mon Sep 26 11:56:30 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign52 assembly : NCBIM34 bias : 5prime chromosome : X id : 34 strand : 1 ------------- Design window length: 1801bp All jobs for probe design are successful - total: 21 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 412 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 : 412/412 Putative probes exceeding selection criteria: 86/412 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 |
|---|---|---|---|---|---|---|
| 36332 | 900 | 29.0 | 4500 | - | 135 | 29.0 |
| 36354 | 850 | 27.4 | 4250 | - | 168 | 27.4 |
| 36355 | 850 | 27.4 | 4250 | - | 210 | 27.4 |
| 36353 | 850 | 27.4 | 4250 | 0.1 | 126 | 27.2 |
| 36377 | 800 | 25.8 | 4000 | - | 160 | 25.8 |
| 36378 | 800 | 25.8 | 4000 | - | 200 | 25.8 |
| 36379 | 800 | 25.8 | 4000 | - | 240 | 25.8 |
| 36333 | 900 | 27.3 | 4500 | 1.1 | 180 | 25.1 |
| 36403 | 750 | 24.2 | 3750 | - | 148 | 24.2 |
| 36404 | 750 | 24.2 | 3750 | - | 185 | 24.2 |
| 36405 | 750 | 24.2 | 3750 | - | 222 | 24.2 |
| 36406 | 750 | 24.2 | 3750 | - | 259 | 24.2 |
| 36407 | 750 | 24.2 | 3750 | - | 296 | 24.2 |
| 36376 | 800 | 25.8 | 4000 | 0.9 | 120 | 24.1 |
| 36313 | 950 | 27.6 | 4750 | 2.2 | 141 | 23.2 |
| 36432 | 700 | 22.6 | 3500 | - | 140 | 22.6 |
| 36433 | 700 | 22.6 | 3500 | - | 175 | 22.6 |
| 36434 | 700 | 22.6 | 3500 | - | 210 | 22.6 |
| 36435 | 700 | 22.6 | 3500 | - | 245 | 22.6 |
| 36436 | 700 | 22.6 | 3500 | - | 280 | 22.6 |
| 36437 | 700 | 22.6 | 3500 | - | 315 | 22.6 |
| 36438 | 700 | 22.6 | 3500 | - | 350 | 22.6 |
| 36380 | 800 | 24.2 | 4000 | 1.2 | 280 | 21.7 |
| 36464 | 650 | 21.0 | 3250 | - | 128 | 21.0 |
| 36465 | 650 | 21.0 | 3250 | - | 160 | 21.0 |
| 36466 | 650 | 21.0 | 3250 | - | 192 | 21.0 |
| 36467 | 650 | 21.0 | 3250 | - | 224 | 21.0 |
| 36468 | 650 | 21.0 | 3250 | - | 256 | 21.0 |
| 36469 | 650 | 21.0 | 3250 | - | 288 | 21.0 |
| 36470 | 650 | 21.0 | 3250 | - | 320 | 21.0 |
| 36471 | 650 | 21.0 | 3250 | - | 352 | 21.0 |
| 36472 | 650 | 21.0 | 3250 | - | 384 | 21.0 |
| 36473 | 650 | 21.0 | 3250 | - | 416 | 21.0 |
| 36402 | 750 | 24.2 | 3750 | 2.1 | 111 | 19.9 |
| 36501 | 600 | 19.4 | 3000 | - | 150 | 19.4 |
| 36502 | 600 | 19.4 | 3000 | - | 180 | 19.4 |
| 36503 | 600 | 19.4 | 3000 | - | 210 | 19.4 |
| 36504 | 600 | 19.4 | 3000 | - | 240 | 19.4 |
| 36505 | 600 | 19.4 | 3000 | - | 270 | 19.4 |
| 36506 | 600 | 19.4 | 3000 | - | 300 | 19.4 |
| 36507 | 600 | 19.4 | 3000 | - | 330 | 19.4 |
| 36508 | 600 | 19.4 | 3000 | - | 360 | 19.4 |
| 36509 | 600 | 19.4 | 3000 | - | 390 | 19.4 |
| 36510 | 600 | 19.4 | 3000 | - | 420 | 19.4 |
| 36511 | 600 | 19.4 | 3000 | - | 450 | 19.4 |
| 36408 | 750 | 22.7 | 3750 | 1.7 | 333 | 19.3 |
| 36312 | 950 | 25.8 | 4750 | 3.5 | 94 | 18.9 |
| 36543 | 550 | 17.7 | 2750 | - | 162 | 17.7 |
| 36544 | 550 | 17.7 | 2750 | - | 189 | 17.7 |
| 36545 | 550 | 17.7 | 2750 | - | 216 | 17.7 |
| 36546 | 550 | 17.7 | 2750 | - | 243 | 17.7 |
| 36547 | 550 | 17.7 | 2750 | - | 270 | 17.7 |
| 36548 | 550 | 17.7 | 2750 | - | 297 | 17.7 |
| 36549 | 550 | 17.7 | 2750 | - | 324 | 17.7 |
| 36550 | 550 | 17.7 | 2750 | - | 351 | 17.7 |
| 36551 | 550 | 17.7 | 2750 | - | 378 | 17.7 |
| 36552 | 550 | 17.7 | 2750 | - | 405 | 17.7 |
| 36553 | 550 | 17.7 | 2750 | - | 432 | 17.7 |
| 36554 | 550 | 17.7 | 2750 | - | 459 | 17.7 |
| 36555 | 550 | 17.7 | 2750 | - | 486 | 17.7 |
| 36556 | 550 | 17.7 | 2750 | - | 513 | 17.7 |
| 36500 | 600 | 19.4 | 3000 | 1.2 | 120 | 17.0 |
| 36439 | 700 | 21.2 | 3500 | 2.1 | 385 | 16.9 |
| 36431 | 700 | 22.6 | 3500 | 3.1 | 105 | 16.3 |
| 36592 | 500 | 16.1 | 2500 | - | 200 | 16.1 |
| 36593 | 500 | 16.1 | 2500 | - | 225 | 16.1 |
| 36594 | 500 | 16.1 | 2500 | - | 250 | 16.1 |
| 36595 | 500 | 16.1 | 2500 | - | 275 | 16.1 |
| 36596 | 500 | 16.1 | 2500 | - | 300 | 16.1 |
| 36597 | 500 | 16.1 | 2500 | - | 325 | 16.1 |
| 36598 | 500 | 16.1 | 2500 | - | 350 | 16.1 |
| 36599 | 500 | 16.1 | 2500 | - | 375 | 16.1 |
| 36600 | 500 | 16.1 | 2500 | - | 400 | 16.1 |
| 36601 | 500 | 16.1 | 2500 | - | 425 | 16.1 |
| 36602 | 500 | 16.1 | 2500 | - | 450 | 16.1 |
| 36603 | 500 | 16.1 | 2500 | - | 475 | 16.1 |
| 36604 | 500 | 16.1 | 2500 | - | 500 | 16.1 |
| 36605 | 500 | 16.1 | 2500 | - | 525 | 16.1 |
| 36606 | 500 | 16.1 | 2500 | - | 550 | 16.1 |
| 36512 | 600 | 18.2 | 3000 | 1.7 | 480 | 14.8 |
| 36356 | 850 | 21.6 | 4250 | 3.8 | 252 | 14.0 |
| 36331 | 900 | 22.1 | 4500 | 4.1 | 90 | 13.8 |
| 36607 | 500 | 15.2 | 2500 | 1.0 | 575 | 13.2 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
| Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
|---|---|---|---|---|---|---|
| 36474 | 650 | 17.8 | 3250 | 4.3 | 448 | 9.1 |
| 36463 | 650 | 18.3 | 3250 | 4.8 | 96 | 8.7 |
| 36557 | 550 | 16.0 | 2750 | 3.6 | 540 | 8.7 |
Overall score = score_ratio - 2 * repetitive DNA content