Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign83 - back to list
Summary
./analyse_probe_search_results : Wed Nov 9 09:33:30 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign83 assembly : NCBIM34 bias : 3prime chromosome : 1 id : 74 strand : 1 ------------- Design window length: 3501bp All jobs for probe design are successful - total: 56 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 1114 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 : 1114/1114 Putative probes that are unique : 0/1114 No putative probes pass with the above criteria Now trying: score-ratio 2, and percent repetitive 40 Putative probes exceeding selection criteria : 27/1114 (both unique and not unique) Putative probes with successfully-picked primers: 26/27 Identified 1 '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/probedesign83.png)
Unique putative probes
No probes
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
70282 | 500 | 15.2 | 2500 | 24.0 | 175 | -32.8 |
70283 | 500 | 14.9 | 2500 | 27.0 | 200 | -39.1 |
70281 | 500 | 11.6 | 2500 | 26.6 | 150 | -41.6 |
70280 | 500 | 8.0 | 2500 | 26.6 | 125 | -45.2 |
70279 | 500 | 6.5 | 2500 | 26.6 | 100 | -46.7 |
70278 | 500 | 5.2 | 2500 | 26.6 | 75 | -48.0 |
70171 | 550 | 13.5 | 2750 | 30.9 | 162 | -48.3 |
70277 | 500 | 4.9 | 2500 | 27.0 | 50 | -49.1 |
70170 | 550 | 10.1 | 2750 | 30.9 | 135 | -51.7 |
70284 | 500 | 9.5 | 2500 | 32.0 | 225 | -54.5 |
70172 | 550 | 8.3 | 2750 | 31.6 | 189 | -55.0 |
70276 | 500 | 4.7 | 2500 | 30.8 | 25 | -56.9 |
70169 | 550 | 7.6 | 2750 | 33.3 | 108 | -58.9 |
70166 | 550 | 5.2 | 2750 | 32.2 | 27 | -59.2 |
70165 | 550 | 5.2 | 2750 | 32.5 | 0 | -59.9 |
70168 | 550 | 6.0 | 2750 | 33.3 | 81 | -60.5 |
70167 | 550 | 5.4 | 2750 | 33.3 | 54 | -61.1 |
70072 | 600 | 9.2 | 3000 | 36.7 | 120 | -64.1 |
70073 | 600 | 8.0 | 3000 | 36.7 | 150 | -65.3 |
70071 | 600 | 7.0 | 3000 | 36.7 | 90 | -66.4 |
70173 | 550 | 6.4 | 2750 | 36.5 | 216 | -66.7 |
70275 | 500 | 4.7 | 2500 | 35.8 | 0 | -66.9 |
70074 | 600 | 6.0 | 3000 | 36.7 | 180 | -67.3 |
70068 | 600 | 5.7 | 3000 | 37.8 | 0 | -70.0 |
70069 | 600 | 5.7 | 3000 | 38.2 | 30 | -70.7 |
70070 | 600 | 6.1 | 3000 | 38.8 | 60 | -71.6 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
70285 | 500 | 6.7 | 2500 | 37.0 | 250 | -67.3 |
Overall score = score_ratio - 2 * repetitive DNA content