Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign29 - back to list
Summary
./analyse_probe_search_results : Mon Sep 5 11:22:00 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign29 assembly : NCBIM34 bias : 3prime chromosome : 17 id : 4 strand : 1 ------------- Design window length: 5190bp All jobs for probe design are successful - total: 70 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 1391 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 3prime end of design window ------------------------ Putative probes without hits : 0 Putative probes with single_self_hit : 1391/1391 Putative probes exceeding selection criteria: 21/1391 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 |
|---|---|---|---|---|---|---|
| 2904 | 700 | 21.5 | 3500 | 3.4 | 490 | 14.6 |
| 3036 | 650 | 19.9 | 3250 | 3.7 | 544 | 12.6 |
| 3034 | 650 | 19.9 | 3250 | 4.5 | 480 | 11.0 |
| 3181 | 600 | 18.4 | 3000 | 4.0 | 600 | 10.4 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
| Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
|---|---|---|---|---|---|---|
| 3035 | 650 | 19.9 | 3250 | 3.7 | 512 | 12.6 |
| 3178 | 600 | 18.4 | 3000 | 4.0 | 510 | 10.4 |
| 3179 | 600 | 18.4 | 3000 | 4.0 | 540 | 10.4 |
| 3180 | 600 | 18.4 | 3000 | 4.0 | 570 | 10.4 |
| 3177 | 600 | 18.9 | 3000 | 4.8 | 480 | 9.2 |
| 3334 | 550 | 17.5 | 2750 | 4.4 | 513 | 8.8 |
| 3335 | 550 | 16.9 | 2750 | 4.4 | 540 | 8.1 |
| 3336 | 550 | 16.9 | 2750 | 4.4 | 567 | 8.1 |
| 3337 | 550 | 16.9 | 2750 | 4.4 | 594 | 8.1 |
| 3338 | 550 | 16.9 | 2750 | 4.4 | 621 | 8.1 |
| 3339 | 550 | 16.9 | 2750 | 4.4 | 648 | 8.1 |
| 3510 | 500 | 15.7 | 2500 | 4.8 | 575 | 6.1 |
| 3511 | 500 | 15.3 | 2500 | 4.8 | 600 | 5.7 |
| 3512 | 500 | 15.3 | 2500 | 4.8 | 625 | 5.7 |
| 3513 | 500 | 15.3 | 2500 | 4.8 | 650 | 5.7 |
| 3514 | 500 | 15.3 | 2500 | 4.8 | 675 | 5.7 |
| 3515 | 500 | 15.3 | 2500 | 4.8 | 700 | 5.7 |
Overall score = score_ratio - 2 * repetitive DNA content