Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign11 - back to list
Summary
./analyse_probe_search_results : Mon Mar 12 15:53:06 2007
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign11 assembly : NCBIM36 bias : 5prime chromosome : X id : 14 strand : 1 ------------- Design window length: 16430bp All jobs for probe design are successful - total: 161 Fetched conf : Exonerate mouse_NCBIM36 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted Fetched 3207 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 : 3207/3207 Putative probes that are unique : 214/3207 Putative probes exceeding selection criteria : 502/3207 (both unique and not unique) Putative probes with successfully-picked primers: 487/502 Identified 79 '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
Unique putative probes
| Putative probe ID | Length | Actual | %rep DNA | Distance |
|---|---|---|---|---|
| 19306 | 1300 | 6500 | - | 8580 |
| 19307 | 1300 | 6500 | - | 8710 |
| 19426 | 1250 | 6250 | - | 8625 |
| 19427 | 1250 | 6250 | - | 8750 |
| 19428 | 1250 | 6250 | - | 8875 |
| 19551 | 1200 | 6000 | - | 8640 |
| 19552 | 1200 | 6000 | - | 8760 |
| 19553 | 1200 | 6000 | - | 8880 |
| 19681 | 1150 | 5750 | - | 8625 |
| 19682 | 1150 | 5750 | - | 8740 |
| 19683 | 1150 | 5750 | - | 8855 |
| 19684 | 1150 | 5750 | - | 8970 |
| 19817 | 1100 | 5500 | - | 8580 |
| 19818 | 1100 | 5500 | - | 8690 |
| 19819 | 1100 | 5500 | - | 8800 |
| 19820 | 1100 | 5500 | - | 8910 |
| 19821 | 1100 | 5500 | - | 9020 |
| 19961 | 1050 | 5250 | - | 8610 |
| 19962 | 1050 | 5250 | - | 8715 |
| 19963 | 1050 | 5250 | - | 8820 |
| 19964 | 1050 | 5250 | - | 8925 |
| 19965 | 1050 | 5250 | - | 9030 |
| 20112 | 1000 | 5000 | - | 8600 |
| 20113 | 1000 | 5000 | - | 8700 |
| 20114 | 1000 | 5000 | - | 8800 |
Putative probes
| Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
|---|---|---|---|---|---|---|
| 19669 | 1150 | 32.5 | 5750 | - | 7245 | 32.5 |
| 20130 | 1000 | 32.5 | 5000 | - | 10400 | 32.5 |
| 19805 | 1100 | 31.1 | 5500 | - | 7260 | 31.1 |
| 20290 | 950 | 30.8 | 4750 | - | 10355 | 30.8 |
| 20291 | 950 | 30.8 | 4750 | - | 10450 | 30.8 |
| 19978 | 1050 | 34.1 | 5250 | 1.9 | 10395 | 30.3 |
| 19833 | 1100 | 32.9 | 5500 | 1.4 | 10340 | 30.2 |
| 19539 | 1200 | 33.9 | 6000 | 2.0 | 7200 | 29.9 |
| 19948 | 1050 | 29.7 | 5250 | - | 7245 | 29.7 |
| 19949 | 1050 | 29.7 | 5250 | - | 7350 | 29.7 |
| 20459 | 900 | 29.2 | 4500 | - | 10350 | 29.2 |
| 20460 | 900 | 29.2 | 4500 | - | 10440 | 29.2 |
| 19806 | 1100 | 31.1 | 5500 | 1.1 | 7370 | 28.9 |
| 19320 | 1300 | 37.8 | 6500 | 4.5 | 10400 | 28.7 |
| 19321 | 1300 | 37.8 | 6500 | 4.5 | 10530 | 28.7 |
| 19322 | 1300 | 37.8 | 6500 | 4.5 | 10660 | 28.7 |
| 19415 | 1250 | 35.3 | 6250 | 3.4 | 7250 | 28.6 |
| 20099 | 1000 | 28.2 | 5000 | - | 7300 | 28.2 |
| 20100 | 1000 | 28.2 | 5000 | - | 7400 | 28.2 |
| 20461 | 900 | 29.2 | 4500 | 0.6 | 10530 | 28.1 |
| 20639 | 850 | 27.6 | 4250 | - | 10370 | 27.6 |
| 20640 | 850 | 27.6 | 4250 | - | 10455 | 27.6 |
| 20641 | 850 | 27.6 | 4250 | - | 10540 | 27.6 |
| 19440 | 1250 | 36.3 | 6250 | 4.7 | 10375 | 26.9 |
| 19441 | 1250 | 36.3 | 6250 | 4.7 | 10500 | 26.9 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
| Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
|---|---|---|---|---|---|---|
| 19967 | 1050 | 29.3 | 5250 | 1.3 | 9240 | 26.7 |
| 19566 | 1200 | 34.9 | 6000 | 4.9 | 10440 | 25.1 |
| 19567 | 1200 | 34.9 | 6000 | 4.9 | 10560 | 25.1 |
| 19568 | 1200 | 34.9 | 6000 | 4.9 | 10680 | 25.1 |
| 20628 | 850 | 27.6 | 4250 | 1.6 | 9435 | 24.3 |
| 20098 | 1000 | 28.2 | 5000 | 2.4 | 7200 | 23.4 |
| 19555 | 1200 | 24.3 | 6000 | 1.2 | 9120 | 22.0 |
| 20920 | 750 | 24.5 | 3750 | 1.3 | 1725 | 21.8 |
| 20424 | 900 | 25.4 | 4500 | 2.7 | 7200 | 20.1 |
| 21131 | 700 | 22.9 | 3500 | 1.4 | 1680 | 20.0 |
| 20119 | 1000 | 22.7 | 5000 | 1.4 | 9300 | 19.9 |
| 20101 | 1000 | 28.2 | 5000 | 4.2 | 7500 | 19.8 |
| 19565 | 1200 | 28.2 | 6000 | 4.9 | 10320 | 18.3 |
| 19823 | 1100 | 19.9 | 5500 | 1.3 | 9240 | 17.4 |
| 20791 | 800 | 22.6 | 4000 | 3.0 | 7200 | 16.6 |
| 21498 | 650 | 21.1 | 3250 | 2.3 | 10790 | 16.5 |
| 21244 | 700 | 19.6 | 3500 | 2.0 | 9590 | 15.6 |
| 20993 | 750 | 21.2 | 3750 | 3.2 | 7200 | 14.8 |
| 20607 | 850 | 24.0 | 4250 | 4.9 | 7650 | 14.1 |
| 19686 | 1150 | 15.7 | 5750 | 1.2 | 9200 | 13.3 |
| 22016 | 550 | 17.9 | 2750 | 2.5 | 9735 | 12.8 |
| 20820 | 800 | 16.2 | 4000 | 1.8 | 9520 | 12.7 |
| 22037 | 550 | 17.9 | 2750 | 2.7 | 10890 | 12.4 |
| 19430 | 1250 | 13.7 | 6250 | 1.1 | 9125 | 11.5 |
| 19431 | 1250 | 13.0 | 6250 | 1.1 | 9250 | 10.8 |
Overall score = score_ratio - 2 * repetitive DNA content