Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign90 - back to list

Summary
Image
Unique putative probes (24)
Putative probes (136)
Redundant probes (86)

Summary

`./analyse_probe_search_results : Tue Dec 20 11:39:03 2005`

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

Fetched probe design: ProbeDesign90
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 5
  id            : 81
  strand        : 1
  -------------

Design window length: 4131bp

All jobs for probe design are successful - total: 69
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1372 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            : 1372/1372
Putative probes that are unique                 : 24/1372
Putative probes exceeding selection criteria    : 246/1372 (both unique and not unique)
Putative probes with successfully-picked primers: 201/246

Identified 86 '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
77007	650	3250	-	1024
77118	600	3000	-	1020
77119	600	3000	-	1050
77120	600	3000	-	1080
77240	550	2750	-	1026
77241	550	2750	-	1053
77242	550	2750	-	1080
77243	550	2750	-	1107
77376	500	2500	-	1025
77377	500	2500	-	1050
77378	500	2500	-	1075
77379	500	2500	-	1100
77380	500	2500	-	1125
77381	500	2500	-	1150
77382	500	2500	-	1175
77404	500	2500	-	1725
77405	500	2500	-	1750
77244	550	2750	0.5	1134
77383	500	2500	3.8	1200
77265	550	2750	3.8	1701
77008	650	3250	3.8	1056
77406	500	2500	4.2	1775
77266	550	2750	4.4	1728
77403	500	2500	4.4	1700

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
76496	950	25.7	4750	-	705	25.7
76120	1300	31.0	6500	3.2	715	24.6
76121	1300	31.0	6500	3.2	780	24.6
76122	1300	31.0	6500	3.2	845	24.6
76123	1300	31.0	6500	3.2	910	24.6
76565	900	24.3	4500	-	720	24.3
76566	900	24.3	4500	-	765	24.3
76432	1000	27.0	5000	1.9	700	23.2
76564	900	24.3	4500	0.6	675	23.2
76164	1250	29.8	6250	3.3	682	23.2
76169	1250	29.8	6250	3.3	992	23.2
76638	850	23.0	4250	-	714	23.0
76639	850	23.0	4250	-	756	23.0
76640	850	23.0	4250	-	798	23.0
76217	1200	28.6	6000	3.4	1020	21.7
76717	800	21.6	4000	-	680	21.6
76718	800	21.6	4000	-	720	21.6
76719	800	21.6	4000	-	760	21.6
76720	800	21.6	4000	-	800	21.6
76721	800	21.6	4000	-	840	21.6
76722	800	21.6	4000	-	880	21.6
76124	1300	31.0	6500	4.8	975	21.4
76497	950	25.7	4750	2.2	752	21.3
76637	850	23.0	4250	0.9	672	21.1
76495	950	25.7	4750	2.3	658	21.0
76431	1000	27.0	5000	3.0	650	21.0
76641	850	23.0	4250	1.1	840	20.9
76803	750	20.3	3750	-	703	20.3
76804	750	20.3	3750	-	740	20.3
76805	750	20.3	3750	-	777	20.3
76806	750	20.3	3750	-	814	20.3
76807	750	20.3	3750	-	851	20.3
76808	750	20.3	3750	-	888	20.3
76809	750	20.3	3750	-	925	20.3
76268	1150	27.4	5750	3.6	1083	20.3
76904	700	19.8	3500	-	980	19.8
77006	650	19.2	3250	-	992	19.2
76896	700	18.9	3500	-	700	18.9
76897	700	18.9	3500	-	735	18.9
76898	700	18.9	3500	-	770	18.9
76899	700	18.9	3500	-	805	18.9
76900	700	18.9	3500	-	840	18.9
76901	700	18.9	3500	-	875	18.9
76902	700	18.9	3500	-	910	18.9
76903	700	18.9	3500	-	945	18.9
76323	1100	26.2	5500	3.8	1155	18.6
77117	600	17.8	3000	-	990	17.8
76997	650	17.6	3250	-	704	17.6
76998	650	17.6	3250	-	736	17.6
76999	650	17.6	3250	-	768	17.6
77000	650	17.6	3250	-	800	17.6
77001	650	17.6	3250	-	832	17.6
77002	650	17.6	3250	-	864	17.6
77003	650	17.6	3250	-	896	17.6
77004	650	17.6	3250	-	928	17.6
77005	650	17.6	3250	-	960	17.6
76381	1050	25.0	5250	3.9	1196	17.2
77169	600	16.9	3000	-	2550	16.9
76371	1050	25.5	5250	4.3	676	16.9
76802	750	20.3	3750	1.9	666	16.5
77239	550	16.3	2750	-	999	16.3
77107	600	16.2	3000	-	690	16.2
77108	600	16.2	3000	-	720	16.2
77109	600	16.2	3000	-	750	16.2
77110	600	16.2	3000	-	780	16.2
77111	600	16.2	3000	-	810	16.2
77112	600	16.2	3000	-	840	16.2
77113	600	16.2	3000	-	870	16.2
77114	600	16.2	3000	-	900	16.2
77115	600	16.2	3000	-	930	16.2
77116	600	16.2	3000	-	960	16.2
77437	500	16.0	2500	-	2550	16.0
77438	500	15.9	2500	-	2575	15.9
76949	700	15.9	3500	-	2555	15.9
77296	550	16.9	2750	0.5	2538	15.8
77055	650	15.8	3250	-	2560	15.8
77297	550	15.7	2750	-	2565	15.7
76443	1000	23.8	5000	4.1	1250	15.6
77298	550	15.5	2750	-	2592	15.5
77439	500	15.2	2500	-	2600	15.2
76996	650	17.6	3250	1.2	672	15.1
77238	550	15.0	2750	-	972	15.0
77170	600	15.0	3000	-	2580	15.0
77228	550	14.9	2750	-	702	14.9
77229	550	14.9	2750	-	729	14.9
77230	550	14.9	2750	-	756	14.9
77231	550	14.9	2750	-	783	14.9
77232	550	14.9	2750	-	810	14.9
77233	550	14.9	2750	-	837	14.9
77234	550	14.9	2750	-	864	14.9
77235	550	14.9	2750	-	891	14.9
77236	550	14.9	2750	-	918	14.9
77237	550	14.9	2750	-	945	14.9
77375	500	14.8	2500	-	1000	14.8
77056	650	14.8	3250	-	2592	14.8
77057	650	14.8	3250	-	2624	14.8
76895	700	18.9	3500	2.1	665	14.6
77171	600	14.6	3000	-	2610	14.6
77440	500	14.1	2500	-	2625	14.1
77441	500	14.1	2500	-	2650	14.1
76508	950	22.6	4750	4.3	1269	14.0
77374	500	13.9	2500	-	975	13.9
77172	600	13.8	3000	-	2640	13.8
77299	550	13.8	2750	-	2619	13.8
77173	600	13.6	3000	-	2670	13.6
77363	500	13.5	2500	-	700	13.5
77364	500	13.5	2500	-	725	13.5
77365	500	13.5	2500	-	750	13.5
77366	500	13.5	2500	-	775	13.5
77367	500	13.5	2500	-	800	13.5
77368	500	13.5	2500	-	825	13.5
77369	500	13.5	2500	-	850	13.5
77370	500	13.5	2500	-	875	13.5
77371	500	13.5	2500	-	900	13.5
77372	500	13.5	2500	-	925	13.5
77373	500	13.5	2500	-	950	13.5
77300	550	13.3	2750	-	2646	13.3
77227	550	14.9	2750	0.9	675	13.0
77301	550	12.6	2750	-	2673	12.6
77442	500	12.5	2500	-	2675	12.5
77302	550	12.5	2750	-	2700	12.5
76579	900	21.4	4500	4.6	1350	12.3
77054	650	16.2	3250	2.0	2528	12.2
77443	500	12.1	2500	-	2700	12.1
77303	550	12.5	2750	0.4	2727	11.8
76950	700	15.9	3500	2.1	2590	11.6
76716	800	21.6	4000	5.0	640	11.6
77362	500	13.5	2500	1.0	675	11.5
77444	500	11.5	2500	-	2725	11.5
77445	500	11.4	2500	-	2750	11.4
77446	500	11.4	2500	-	2775	11.4
76852	750	17.0	3750	3.3	2516	10.4
76948	700	16.1	3500	3.0	2520	10.1
77436	500	16.0	2500	3.2	2525	9.6
76853	750	17.0	3750	3.7	2553	9.6
77058	650	14.8	3250	4.8	2656	5.2

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
76165	1250	29.8	6250	3.3	744	23.2
76166	1250	29.8	6250	3.3	806	23.2
76167	1250	29.8	6250	3.3	868	23.2
76168	1250	29.8	6250	3.3	930	23.2
76212	1200	28.6	6000	3.4	720	21.7
76213	1200	28.6	6000	3.4	780	21.7
76214	1200	28.6	6000	3.4	840	21.7
76215	1200	28.6	6000	3.4	900	21.7
76216	1200	28.6	6000	3.4	960	21.7
76261	1150	27.4	5750	3.6	684	20.3
76262	1150	27.4	5750	3.6	741	20.3
76263	1150	27.4	5750	3.6	798	20.3
76264	1150	27.4	5750	3.6	855	20.3
76265	1150	27.4	5750	3.6	912	20.3
76266	1150	27.4	5750	3.6	969	20.3
76267	1150	27.4	5750	3.6	1026	20.3
76315	1100	26.2	5500	3.7	715	18.7
76316	1100	26.2	5500	3.7	770	18.7
76317	1100	26.2	5500	3.7	825	18.7
76318	1100	26.2	5500	3.7	880	18.7
76319	1100	26.2	5500	3.7	935	18.7
76320	1100	26.2	5500	3.7	990	18.7
76321	1100	26.2	5500	3.7	1045	18.7
76322	1100	26.2	5500	3.7	1100	18.7
76567	900	24.3	4500	3.2	810	17.9
76372	1050	25.0	5250	3.9	728	17.2
76373	1050	25.0	5250	3.9	780	17.2
76374	1050	25.0	5250	3.9	832	17.2
76375	1050	25.0	5250	3.9	884	17.2
76376	1050	25.0	5250	3.9	936	17.2
76377	1050	25.0	5250	3.9	988	17.2
76378	1050	25.0	5250	3.9	1040	17.2
76379	1050	25.0	5250	3.9	1092	17.2
76380	1050	25.0	5250	3.9	1144	17.2
76433	1000	23.8	5000	4.1	750	15.6
76434	1000	23.8	5000	4.1	800	15.6
76435	1000	23.8	5000	4.1	850	15.6
76436	1000	23.8	5000	4.1	900	15.6
76437	1000	23.8	5000	4.1	950	15.6
76438	1000	23.8	5000	4.1	1000	15.6
76439	1000	23.8	5000	4.1	1050	15.6
76440	1000	23.8	5000	4.1	1100	15.6
76441	1000	23.8	5000	4.1	1150	15.6
76442	1000	23.8	5000	4.1	1200	15.6
76498	950	22.6	4750	4.3	799	14.0
76499	950	22.6	4750	4.3	846	14.0
76500	950	22.6	4750	4.3	893	14.0
76501	950	22.6	4750	4.3	940	14.0
76502	950	22.6	4750	4.3	987	14.0
76503	950	22.6	4750	4.3	1034	14.0
76504	950	22.6	4750	4.3	1081	14.0
76505	950	22.6	4750	4.3	1128	14.0
76506	950	22.6	4750	4.3	1175	14.0
76507	950	22.6	4750	4.3	1222	14.0
76568	900	21.4	4500	4.6	855	12.3
76569	900	21.4	4500	4.6	900	12.3
76570	900	21.4	4500	4.6	945	12.3
76571	900	21.4	4500	4.6	990	12.3
76572	900	21.4	4500	4.6	1035	12.3
76573	900	21.4	4500	4.6	1080	12.3
76574	900	21.4	4500	4.6	1125	12.3
76575	900	21.4	4500	4.6	1170	12.3
76576	900	21.4	4500	4.6	1215	12.3
76577	900	21.4	4500	4.6	1260	12.3
76578	900	21.4	4500	4.6	1305	12.3
76810	750	20.3	3750	4.1	962	12.0
76723	800	20.5	4000	4.9	920	10.8
76642	850	20.2	4250	4.8	882	10.6
76643	850	20.2	4250	4.8	924	10.6
76644	850	20.2	4250	4.8	966	10.6
76645	850	20.2	4250	4.8	1008	10.6
76646	850	20.2	4250	4.8	1050	10.6
76647	850	20.2	4250	4.8	1092	10.6
76648	850	20.2	4250	4.8	1134	10.6
76649	850	20.2	4250	4.8	1176	10.6
76650	850	20.2	4250	4.8	1218	10.6
76651	850	20.2	4250	4.8	1260	10.6
76652	850	20.2	4250	4.8	1302	10.6
76653	850	20.2	4250	4.8	1344	10.6
76654	850	20.2	4250	4.8	1386	10.6
76905	700	19.9	3500	4.9	1015	10.2
77168	600	16.9	3000	3.5	2520	9.9
77106	600	16.2	3000	3.3	660	9.5
77121	600	19.1	3000	4.8	1110	9.4
77174	600	13.6	3000	4.2	2700	5.3
77447	500	11.4	2500	5.0	2800	1.4

Overall score = score_ratio - 2 * repetitive DNA content