Automated design of genomic Southern blot probes

Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant

Design Case - ProbeDesign16 - back to list

Summary
Image
Unique putative probes (156)
Putative probes (316)
Redundant probes (248)

Summary

`./analyse_probe_search_results : Tue Feb 13 12:54:38 2007`

Connected to host: host, as user: user
Database       : southern_blot_designs

Fetched probe design: ProbeDesign16
  assembly      : NCBIM36
  bias          : 5prime
  chromosome    : 16
  id            : 3
  strand        : 1
  -------------

Design window length: 4260bp

All jobs for probe design are successful - total: 72
Fetched conf : Exonerate mouse_NCBIM36 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 1423 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            : 1423/1423
Putative probes that are unique                 : 156/1423
Putative probes exceeding selection criteria    : 720/1423 (both unique and not unique)
Putative probes with successfully-picked primers: 500/720

Identified 248 '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
2707	900	4500	-	3330
2749	850	4250	-	1722
2750	850	4250	-	1764
2787	850	4250	-	3318
2788	850	4250	-	3360
2789	850	4250	-	3402
2833	800	4000	-	1720
2834	800	4000	-	1760
2835	800	4000	-	1800
2873	800	4000	-	3320
2874	800	4000	-	3360
2875	800	4000	-	3400
2876	800	4000	-	3440
2924	750	3750	-	1739
2925	750	3750	-	1776
2926	750	3750	-	1813
2927	750	3750	-	1850
2967	750	3750	-	3330
2968	750	3750	-	3367
2969	750	3750	-	3404
2970	750	3750	-	3441
2971	750	3750	-	3478
3021	700	3500	-	1715
3022	700	3500	-	1750
3023	700	3500	-	1785

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
2269	1250	35.9	6250	-	2976	35.9
2220	1300	37.4	6500	0.8	2925	35.7
2319	1200	34.5	6000	-	2940	34.5
2320	1200	34.5	6000	-	3000	34.5
2373	1150	33.0	5750	-	2964	33.0
2374	1150	33.0	5750	-	3021	33.0
2375	1150	33.0	5750	-	3078	33.0
2186	1300	37.6	6500	2.3	715	33.0
2187	1300	37.6	6500	2.3	780	33.0
2188	1300	37.6	6500	2.3	845	33.0
2189	1300	37.6	6500	2.3	910	33.0
2190	1300	37.6	6500	2.3	975	33.0
2191	1300	37.6	6500	2.3	1040	33.0
2192	1300	37.6	6500	2.3	1105	33.0
2193	1300	37.6	6500	2.3	1170	33.0
2194	1300	37.6	6500	2.3	1235	33.0
2195	1300	37.6	6500	2.3	1300	33.0
2185	1300	37.6	6500	2.8	650	31.9
2430	1100	31.6	5500	-	2970	31.6
2431	1100	31.6	5500	-	3025	31.6
2432	1100	31.6	5500	-	3080	31.6
2433	1100	31.6	5500	-	3135	31.6
2196	1300	37.6	6500	3.0	1365	31.6
2232	1250	36.1	6250	2.4	682	31.3
2243	1250	36.1	6250	2.4	1364	31.3

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
2233	1250	36.1	6250	2.4	744	31.3
2234	1250	36.1	6250	2.4	806	31.3
2235	1250	36.1	6250	2.4	868	31.3
2236	1250	36.1	6250	2.4	930	31.3
2237	1250	36.1	6250	2.4	992	31.3
2238	1250	36.1	6250	2.4	1054	31.3
2239	1250	36.1	6250	2.4	1116	31.3
2240	1250	36.1	6250	2.4	1178	31.3
2241	1250	36.1	6250	2.4	1240	31.3
2242	1250	36.1	6250	2.4	1302	31.3
2283	1200	34.7	6000	2.5	780	29.7
2284	1200	34.7	6000	2.5	840	29.7
2285	1200	34.7	6000	2.5	900	29.7
2286	1200	34.7	6000	2.5	960	29.7
2287	1200	34.7	6000	2.5	1020	29.7
2288	1200	34.7	6000	2.5	1080	29.7
2289	1200	34.7	6000	2.5	1140	29.7
2290	1200	34.7	6000	2.5	1200	29.7
2291	1200	34.7	6000	2.5	1260	29.7
2292	1200	34.7	6000	2.5	1320	29.7
2293	1200	34.7	6000	2.5	1380	29.7
2336	1150	33.2	5750	2.6	855	28.0
2337	1150	33.2	5750	2.6	912	28.0
2338	1150	33.2	5750	2.6	969	28.0
2339	1150	33.2	5750	2.6	1026	28.0

Overall score = score_ratio - 2 * repetitive DNA content