Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign38 - back to list
Summary
./analyse_probe_search_results : Mon Sep 5 11:38:41 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign38 assembly : NCBIM34 bias : 5prime chromosome : X id : 14 strand : 1 ------------- Design window length: 2001bp All jobs for probe design are successful - total: 28 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 557 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 : 557/557 Putative probes exceeding selection criteria: 30/557 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 |
|---|---|---|---|---|---|---|
| 18818 | 600 | 18.0 | 3000 | - | 1230 | 18.0 |
| 18927 | 500 | 16.7 | 2500 | - | 1225 | 16.7 |
| 18870 | 550 | 16.5 | 2750 | - | 1242 | 16.5 |
| 18871 | 550 | 16.5 | 2750 | - | 1269 | 16.5 |
| 18872 | 550 | 16.5 | 2750 | - | 1296 | 16.5 |
| 18819 | 600 | 18.0 | 3000 | 0.8 | 1260 | 16.3 |
| 18928 | 500 | 15.4 | 2500 | - | 1250 | 15.4 |
| 18997 | 450 | 15.0 | 2250 | - | 1276 | 15.0 |
| 18929 | 500 | 15.0 | 2500 | - | 1275 | 15.0 |
| 18930 | 500 | 15.0 | 2500 | - | 1300 | 15.0 |
| 18931 | 500 | 15.0 | 2500 | - | 1325 | 15.0 |
| 18932 | 500 | 15.0 | 2500 | - | 1350 | 15.0 |
| 18998 | 450 | 14.2 | 2250 | - | 1298 | 14.2 |
| 18772 | 650 | 19.5 | 3250 | 2.6 | 1216 | 14.2 |
| 18869 | 550 | 16.5 | 2750 | 1.3 | 1215 | 13.9 |
| 18999 | 450 | 13.5 | 2250 | - | 1320 | 13.5 |
| 19000 | 450 | 13.5 | 2250 | - | 1342 | 13.5 |
| 19001 | 450 | 13.5 | 2250 | - | 1364 | 13.5 |
| 19002 | 450 | 13.5 | 2250 | - | 1386 | 13.5 |
| 19077 | 400 | 12.8 | 2000 | - | 1340 | 12.8 |
| 19003 | 450 | 13.5 | 2250 | 0.7 | 1408 | 12.1 |
| 19078 | 400 | 12.0 | 2000 | - | 1360 | 12.0 |
| 19079 | 400 | 12.0 | 2000 | - | 1380 | 12.0 |
| 19080 | 400 | 12.0 | 2000 | - | 1400 | 12.0 |
| 19081 | 400 | 12.0 | 2000 | - | 1420 | 12.0 |
| 19082 | 400 | 12.0 | 2000 | - | 1440 | 12.0 |
| 18817 | 600 | 18.0 | 3000 | 3.7 | 1200 | 10.6 |
| 18873 | 550 | 16.5 | 2750 | 3.3 | 1323 | 9.9 |
| 19083 | 400 | 12.0 | 2000 | 1.2 | 1460 | 9.5 |
| 18933 | 500 | 15.0 | 2500 | 4.0 | 1375 | 7.0 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
No probes
Overall score = score_ratio - 2 * repetitive DNA content