Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign58 - back to list
Summary
./analyse_probe_search_results : Thu Sep 29 17:24:04 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign58 assembly : NCBIM34 bias : 5prime chromosome : 10 id : 45 strand : 1 ------------- Design window length: 3001bp All jobs for probe design are successful - total: 46 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 907 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 : 907/907 Putative probes exceeding selection criteria: 15/907 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 |
---|---|---|---|---|---|---|
47061 | 600 | 18.5 | 3000 | 0.3 | 1680 | 17.9 |
47148 | 550 | 17.3 | 2750 | - | 1674 | 17.3 |
47149 | 550 | 17.0 | 2750 | - | 1701 | 17.0 |
47150 | 550 | 17.0 | 2750 | - | 1728 | 17.0 |
47060 | 600 | 17.8 | 3000 | 0.7 | 1650 | 16.4 |
47244 | 500 | 15.7 | 2500 | - | 1675 | 15.7 |
47245 | 500 | 15.7 | 2500 | - | 1700 | 15.7 |
47246 | 500 | 15.7 | 2500 | - | 1725 | 15.7 |
47247 | 500 | 15.4 | 2500 | - | 1750 | 15.4 |
47248 | 500 | 15.4 | 2500 | - | 1775 | 15.4 |
47147 | 550 | 16.3 | 2750 | 1.3 | 1647 | 13.7 |
47243 | 500 | 14.8 | 2500 | 0.8 | 1650 | 13.2 |
46982 | 650 | 19.2 | 3250 | 4.0 | 1632 | 11.2 |
47151 | 550 | 16.7 | 2750 | 4.9 | 1755 | 6.8 |
47249 | 500 | 15.4 | 2500 | 4.4 | 1800 | 6.6 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
No probes
Overall score = score_ratio - 2 * repetitive DNA content