Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign21 - back to list

Summary
Image
Unique putative probes (22)
Putative probes (126)
Redundant probes (48)

Summary

`./analyse_probe_search_results : Tue Dec 19 12:01:57 2006`

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

Fetched probe design: ProbeDesign21
  assembly      : NCBIM36
  bias          : 3prime
  chromosome    : 16
  id            : 1
  strand        : 1
  -------------

Design window length: 3717bp

All jobs for probe design are successful - total: 60
Fetched conf : Exonerate mouse_NCBIM36 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 1200 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            : 1200/1200
Putative probes that are unique                 : 22/1200
Putative probes exceeding selection criteria    : 196/1200 (both unique and not unique)
Putative probes with successfully-picked primers: 194/196

Identified 48 '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
922	600	3000	-	2160
1034	550	2750	-	2160
1035	550	2750	-	2187
1036	550	2750	-	2214
1123	500	2500	-	1275
1124	500	2500	-	1300
1158	500	2500	-	2150
1159	500	2500	-	2175
1160	500	2500	-	2200
1161	500	2500	-	2225
1162	500	2500	-	2250
1184	500	2500	-	2800
1185	500	2500	-	2825
1163	500	2500	0.2	2275
1001	550	2750	1.1	1269
1125	500	2500	2.4	1325
1057	550	2750	2.7	2781
1122	500	2500	3.8	1250
1000	550	2750	4.9	1242
1002	550	2750	6.0	1296
1126	500	2500	7.4	1350
892	600	3000	9.3	1260

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
114	1200	35.1	6000	2.2	2100	30.6
158	1150	33.6	5750	1.9	2109	29.8
159	1150	33.6	5750	1.9	2166	29.8
206	1100	32.2	5500	2.0	2145	28.2
207	1100	32.2	5500	2.0	2200	28.2
256	1050	30.7	5250	2.1	2132	26.5
257	1050	30.7	5250	2.1	2184	26.5
258	1050	30.7	5250	2.1	2236	26.5
205	1100	32.2	5500	3.4	2090	25.4
259	1050	30.7	5250	2.8	2288	25.2
310	1000	29.2	5000	2.2	2150	24.8
311	1000	29.2	5000	2.2	2200	24.8
312	1000	29.2	5000	2.2	2250	24.8
313	1000	29.2	5000	2.2	2300	24.8
367	950	27.8	4750	2.3	2115	23.1
368	950	27.8	4750	2.3	2162	23.1
369	950	27.8	4750	2.3	2209	23.1
370	950	27.8	4750	2.3	2256	23.1
371	950	27.8	4750	2.3	2303	23.1
372	950	27.8	4750	2.3	2350	23.1
255	1050	30.7	5250	4.5	2080	21.7
428	900	26.3	4500	2.4	2115	21.4
429	900	26.3	4500	2.4	2160	21.4
430	900	26.3	4500	2.4	2205	21.4
431	900	26.3	4500	2.4	2250	21.4
432	900	26.3	4500	2.4	2295	21.4
433	900	26.3	4500	2.4	2340	21.4
434	900	26.3	4500	2.4	2385	21.4
435	900	26.3	4500	2.4	2430	21.4
73	1250	29.2	6250	3.9	2108	21.4
820	650	20.2	3250	-	2112	20.2
495	850	24.9	4250	2.6	2142	19.7
496	850	24.9	4250	2.6	2184	19.7
497	850	24.9	4250	2.6	2226	19.7
498	850	24.9	4250	2.6	2268	19.7
499	850	24.9	4250	2.6	2310	19.7
500	850	24.9	4250	2.6	2352	19.7
501	850	24.9	4250	2.6	2394	19.7
502	850	24.9	4250	2.6	2436	19.7
503	850	24.9	4250	2.6	2478	19.7
921	600	18.8	3000	-	2130	18.8
115	1200	26.8	6000	4.2	2160	18.3
566	800	23.4	4000	2.8	2120	17.9
567	800	23.4	4000	2.8	2160	17.9
568	800	23.4	4000	2.8	2200	17.9
569	800	23.4	4000	2.8	2240	17.9
570	800	23.4	4000	2.8	2280	17.9
571	800	23.4	4000	2.8	2320	17.9
572	800	23.4	4000	2.8	2360	17.9
573	800	23.4	4000	2.8	2400	17.9
574	800	23.4	4000	2.8	2440	17.9
575	800	23.4	4000	2.8	2480	17.9
576	800	23.4	4000	2.8	2520	17.9
1033	550	17.2	2750	-	2133	17.2
920	600	18.8	3000	0.8	2100	17.1
643	750	21.9	3750	2.9	2109	16.1
644	750	21.9	3750	2.9	2146	16.1
645	750	21.9	3750	2.9	2183	16.1
646	750	21.9	3750	2.9	2220	16.1
647	750	21.9	3750	2.9	2257	16.1
648	750	21.9	3750	2.9	2294	16.1
649	750	21.9	3750	2.9	2331	16.1
650	750	21.9	3750	2.9	2368	16.1
651	750	21.9	3750	2.9	2405	16.1
652	750	21.9	3750	2.9	2442	16.1
653	750	21.9	3750	2.9	2479	16.1
654	750	21.9	3750	2.9	2516	16.1
655	750	21.9	3750	2.9	2553	16.1
1032	550	15.8	2750	-	2106	15.8
1157	500	15.6	2500	-	2125	15.6
728	700	20.5	3500	3.1	2135	14.2
729	700	20.5	3500	3.1	2170	14.2
730	700	20.5	3500	3.1	2205	14.2
731	700	20.5	3500	3.1	2240	14.2
732	700	20.5	3500	3.1	2275	14.2
733	700	20.5	3500	3.1	2310	14.2
734	700	20.5	3500	3.1	2345	14.2
735	700	20.5	3500	3.1	2380	14.2
736	700	20.5	3500	3.1	2415	14.2
737	700	20.5	3500	3.1	2450	14.2
738	700	20.5	3500	3.1	2485	14.2
739	700	20.5	3500	3.1	2520	14.2
740	700	20.5	3500	3.1	2555	14.2
741	700	20.5	3500	3.1	2590	14.2
742	700	20.5	3500	3.1	2625	14.2
821	650	20.2	3250	3.1	2144	14.0
1156	500	15.6	2500	1.0	2100	13.6
923	600	18.6	3000	2.7	2190	13.3
819	650	20.3	3250	3.8	2080	12.6
822	650	19.0	3250	3.4	2176	12.2
823	650	19.0	3250	3.4	2208	12.2
824	650	19.0	3250	3.4	2240	12.2
825	650	19.0	3250	3.4	2272	12.2
826	650	19.0	3250	3.4	2304	12.2
827	650	19.0	3250	3.4	2336	12.2
828	650	19.0	3250	3.4	2368	12.2
829	650	19.0	3250	3.4	2400	12.2
830	650	19.0	3250	3.4	2432	12.2
831	650	19.0	3250	3.4	2464	12.2
832	650	19.0	3250	3.4	2496	12.2
833	650	19.0	3250	3.4	2528	12.2
834	650	19.0	3250	3.4	2560	12.2
835	650	19.0	3250	3.4	2592	12.2
836	650	19.0	3250	3.4	2624	12.2
837	650	19.0	3250	3.4	2656	12.2
1037	550	17.1	2750	3.1	2241	10.9
924	600	17.5	3000	3.7	2220	10.2
925	600	17.5	3000	3.7	2250	10.2
926	600	17.5	3000	3.7	2280	10.2
927	600	17.5	3000	3.7	2310	10.2
928	600	17.5	3000	3.7	2340	10.2
929	600	17.5	3000	3.7	2370	10.2
930	600	17.5	3000	3.7	2400	10.2
931	600	17.5	3000	3.7	2430	10.2
932	600	17.5	3000	3.7	2460	10.2
933	600	17.5	3000	3.7	2490	10.2
934	600	17.5	3000	3.7	2520	10.2
935	600	17.5	3000	3.7	2550	10.2
936	600	17.5	3000	3.7	2580	10.2
937	600	17.5	3000	3.7	2610	10.2
938	600	17.5	3000	3.7	2640	10.2
939	600	17.5	3000	3.7	2670	10.2
940	600	17.5	3000	3.7	2700	10.2
941	600	17.5	3000	3.7	2730	10.2
1031	550	17.2	2750	4.7	2079	7.7
1186	500	14.4	2500	3.8	2850	6.8

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
309	1000	29.2	5000	2.7	2100	23.8
314	1000	28.7	5000	4.1	2350	20.5
373	950	27.8	4750	4.0	2397	19.8
208	1100	27.6	5500	4.2	2255	19.3
494	850	24.9	4250	3.2	2100	18.5
656	750	21.9	3750	4.1	2590	13.7
727	700	21.0	3500	3.9	2100	13.2
838	650	19.0	3250	4.5	2688	10.1
1056	550	16.8	2750	4.0	2754	8.8
1038	550	16.1	2750	4.0	2268	8.1
1039	550	16.1	2750	4.0	2295	8.1
1040	550	16.1	2750	4.0	2322	8.1
1041	550	16.1	2750	4.0	2349	8.1
1042	550	16.1	2750	4.0	2376	8.1
1043	550	16.1	2750	4.0	2403	8.1
1044	550	16.1	2750	4.0	2430	8.1
1045	550	16.1	2750	4.0	2457	8.1
1046	550	16.1	2750	4.0	2484	8.1
1047	550	16.1	2750	4.0	2511	8.1
1048	550	16.1	2750	4.0	2538	8.1
1049	550	16.1	2750	4.0	2565	8.1
1050	550	16.1	2750	4.0	2592	8.1
1051	550	16.1	2750	4.0	2619	8.1
1052	550	16.1	2750	4.0	2646	8.1
1053	550	16.1	2750	4.0	2673	8.1
1054	550	16.1	2750	4.0	2700	8.1
1055	550	16.1	2750	4.0	2727	8.1
1183	500	15.7	2500	4.2	2775	7.3
1182	500	15.1	2500	4.4	2750	6.3
1164	500	15.0	2500	4.4	2300	6.2
1165	500	14.6	2500	4.4	2325	5.8
1166	500	14.6	2500	4.4	2350	5.8
1167	500	14.6	2500	4.4	2375	5.8
1168	500	14.6	2500	4.4	2400	5.8
1169	500	14.6	2500	4.4	2425	5.8
1170	500	14.6	2500	4.4	2450	5.8
1171	500	14.6	2500	4.4	2475	5.8
1172	500	14.6	2500	4.4	2500	5.8
1173	500	14.6	2500	4.4	2525	5.8
1174	500	14.6	2500	4.4	2550	5.8
1175	500	14.6	2500	4.4	2575	5.8
1176	500	14.6	2500	4.4	2600	5.8
1177	500	14.6	2500	4.4	2625	5.8
1178	500	14.6	2500	4.4	2650	5.8
1179	500	14.6	2500	4.4	2675	5.8
1180	500	14.6	2500	4.4	2700	5.8
1181	500	14.6	2500	4.4	2725	5.8
1058	550	12.9	2750	4.9	2808	3.0

Overall score = score_ratio - 2 * repetitive DNA content