Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign36 - back to list
Summary
./analyse_probe_search_results : Mon Sep 5 11:31:44 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign36 assembly : NCBIM34 bias : 5prime chromosome : X id : 12 strand : 1 ------------- Design window length: 1204bp All jobs for probe design are successful - total: 12 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 235 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 : 235/235 No putative probes pass with the above criteria Using: score-ratio 2, and percent repetitive 40 Putative probes exceeding selection criteria: 23/235 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 |
---|---|---|---|---|---|---|
11282 | 400 | 3.6 | 2000 | 1.5 | 800 | 0.6 |
11281 | 400 | 3.6 | 2000 | 6.5 | 780 | -9.4 |
11280 | 400 | 3.6 | 2000 | 11.5 | 760 | -19.4 |
11241 | 450 | 4.1 | 2250 | 12.9 | 748 | -21.7 |
11279 | 400 | 3.6 | 2000 | 16.5 | 740 | -29.4 |
11240 | 450 | 4.1 | 2250 | 17.8 | 726 | -31.5 |
11206 | 500 | 4.5 | 2500 | 21.2 | 700 | -37.9 |
11278 | 400 | 3.6 | 2000 | 21.5 | 720 | -39.4 |
11239 | 450 | 4.1 | 2250 | 22.7 | 704 | -41.3 |
11205 | 500 | 4.5 | 2500 | 26.2 | 675 | -47.9 |
11277 | 400 | 3.6 | 2000 | 26.5 | 700 | -49.4 |
11238 | 450 | 4.1 | 2250 | 27.6 | 682 | -51.0 |
11177 | 550 | 4.8 | 2750 | 28.7 | 648 | -52.7 |
11204 | 500 | 4.4 | 2500 | 31.2 | 650 | -58.0 |
11276 | 400 | 3.6 | 2000 | 31.5 | 680 | -59.4 |
11237 | 450 | 4.1 | 2250 | 32.4 | 660 | -60.8 |
11176 | 550 | 4.1 | 2750 | 33.6 | 621 | -63.2 |
11152 | 600 | 4.4 | 3000 | 34.3 | 600 | -64.3 |
11203 | 500 | 3.8 | 2500 | 36.2 | 625 | -68.6 |
11275 | 400 | 3.6 | 2000 | 36.5 | 660 | -69.4 |
11236 | 450 | 3.7 | 2250 | 37.3 | 638 | -71.0 |
11175 | 550 | 4.0 | 2750 | 38.5 | 594 | -73.1 |
11151 | 600 | 3.9 | 3000 | 39.3 | 570 | -74.7 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
No probes
Overall score = score_ratio - 2 * repetitive DNA content