Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign99 - back to list

Summary
Image
Unique putative probes (59)
Putative probes (91)
Redundant probes (139)

Summary

`./analyse_probe_search_results : Tue Jan 31 11:07:06 2006`

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

Fetched probe design: ProbeDesign99
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 9
  id            : 100
  strand        : 1
  -------------

Design window length: 1501bp

All jobs for probe design are successful - total: 15
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 289 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            : 289/289
Putative probes that are unique                 : 59/289
Putative probes exceeding selection criteria    : 289/289 (both unique and not unique)
Putative probes with successfully-picked primers: 271/289

Identified 139 '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
95002	850	4250	-	252
95019	800	4000	-	280
95020	800	4000	-	320
95037	750	3750	-	259
95038	750	3750	-	296
95039	750	3750	-	333
95040	750	3750	-	370
95059	700	3500	-	280
95060	700	3500	-	315
95061	700	3500	-	350
95062	700	3500	-	385
95063	700	3500	-	420
95082	650	3250	-	256
95083	650	3250	-	288
95084	650	3250	-	320
95085	650	3250	-	352
95086	650	3250	-	384
95087	650	3250	-	416
95088	650	3250	-	448
95110	600	3000	-	270
95111	600	3000	-	300
95112	600	3000	-	330
95113	600	3000	-	360
95114	600	3000	-	390
95115	600	3000	-	420
95116	600	3000	-	450
95117	600	3000	-	480
95118	600	3000	-	510
95142	550	2750	-	270
95143	550	2750	-	297
95144	550	2750	-	324
95145	550	2750	-	351
95146	550	2750	-	378
95147	550	2750	-	405
95148	550	2750	-	432
95149	550	2750	-	459
95150	550	2750	-	486
95151	550	2750	-	513
95152	550	2750	-	540
95153	550	2750	-	567
95179	500	2500	-	275
95180	500	2500	-	300
95181	500	2500	-	325
95182	500	2500	-	350
95183	500	2500	-	375
95184	500	2500	-	400
95185	500	2500	-	425
95186	500	2500	-	450
95187	500	2500	-	475
95188	500	2500	-	500
95189	500	2500	-	525
95190	500	2500	-	550
95191	500	2500	-	575
95192	500	2500	-	600
95193	500	2500	0.2	625
95089	650	3250	0.9	480
95003	850	4250	2.0	294
95119	600	3000	2.7	540
95154	550	2750	3.1	594

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
94942	1100	35.5	5500	-	0	35.5
94950	1050	33.9	5250	-	0	33.9
94951	1050	33.9	5250	-	52	33.9
94959	1000	32.3	5000	-	0	32.3
94960	1000	32.3	5000	-	50	32.3
94961	1000	32.3	5000	-	100	32.3
94920	1300	34.2	6500	1.3	0	31.6
94921	1300	34.2	6500	1.3	65	31.6
94922	1300	34.2	6500	1.3	130	31.6
94923	1300	34.2	6500	1.3	195	31.6
94970	950	30.6	4750	-	0	30.6
94971	950	30.6	4750	-	47	30.6
94972	950	30.6	4750	-	94	30.6
94973	950	30.6	4750	-	141	30.6
94925	1250	32.9	6250	1.4	62	30.2
94926	1250	32.9	6250	1.4	124	30.2
94927	1250	32.9	6250	1.4	186	30.2
94928	1250	32.9	6250	1.4	248	30.2
94986	900	29.4	4500	-	180	29.4
94987	900	29.4	4500	0.1	225	29.2
94982	900	29.0	4500	-	0	29.0
94983	900	29.0	4500	-	45	29.0
94984	900	29.0	4500	-	90	29.0
94985	900	29.0	4500	-	135	29.0
94934	1200	31.6	6000	1.4	300	28.7
95000	850	27.8	4250	-	168	27.8
95001	850	27.8	4250	-	210	27.8
94996	850	27.4	4250	-	0	27.4
94997	850	27.4	4250	-	42	27.4
94998	850	27.4	4250	-	84	27.4
94999	850	27.4	4250	-	126	27.4
95016	800	26.1	4000	-	160	26.1
95017	800	26.1	4000	-	200	26.1
95018	800	26.1	4000	-	240	26.1
95012	800	25.8	4000	-	0	25.8
95013	800	25.8	4000	-	40	25.8
95014	800	25.8	4000	-	80	25.8
95015	800	25.8	4000	-	120	25.8
95034	750	24.5	3750	-	148	24.5
95035	750	24.5	3750	-	185	24.5
95036	750	24.5	3750	-	222	24.5
95030	750	24.2	3750	-	0	24.2
95031	750	24.2	3750	-	37	24.2
95032	750	24.2	3750	-	74	24.2
95033	750	24.2	3750	-	111	24.2
95056	700	22.9	3500	-	175	22.9
95057	700	22.9	3500	-	210	22.9
95058	700	22.9	3500	-	245	22.9
95051	700	22.6	3500	-	0	22.6
95052	700	22.6	3500	-	35	22.6
95053	700	22.6	3500	-	70	22.6
95054	700	22.6	3500	-	105	22.6
95055	700	22.6	3500	-	140	22.6
95079	650	21.2	3250	-	160	21.2
95080	650	21.2	3250	-	192	21.2
95081	650	21.2	3250	-	224	21.2
95074	650	21.0	3250	-	0	21.0
95075	650	21.0	3250	-	32	21.0
95076	650	21.0	3250	-	64	21.0
95077	650	21.0	3250	-	96	21.0
95078	650	21.0	3250	-	128	21.0
95106	600	19.6	3000	-	150	19.6
95107	600	19.6	3000	-	180	19.6
95108	600	19.6	3000	-	210	19.6
95109	600	19.6	3000	-	240	19.6
95101	600	19.4	3000	-	0	19.4
95102	600	19.4	3000	-	30	19.4
95103	600	19.4	3000	-	60	19.4
95104	600	19.4	3000	-	90	19.4
95105	600	19.4	3000	-	120	19.4
95138	550	18.0	2750	-	162	18.0
95139	550	18.0	2750	-	189	18.0
95140	550	18.0	2750	-	216	18.0
95141	550	18.0	2750	-	243	18.0
95132	550	17.7	2750	-	0	17.7
95133	550	17.7	2750	-	27	17.7
95134	550	17.7	2750	-	54	17.7
95135	550	17.7	2750	-	81	17.7
95136	550	17.7	2750	-	108	17.7
95137	550	17.7	2750	-	135	17.7
95174	500	16.3	2500	-	150	16.3
95175	500	16.3	2500	-	175	16.3
95176	500	16.3	2500	-	200	16.3
95177	500	16.3	2500	-	225	16.3
95178	500	16.3	2500	-	250	16.3
95168	500	16.1	2500	-	0	16.1
95169	500	16.1	2500	-	25	16.1
95170	500	16.1	2500	-	50	16.1
95171	500	16.1	2500	-	75	16.1
95172	500	16.1	2500	-	100	16.1
95173	500	16.1	2500	-	125	16.1

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
94935	1150	37.1	5750	1.5	0	34.1
94943	1100	35.5	5500	1.5	55	32.4
94952	1050	33.9	5250	1.6	104	30.6
94924	1250	32.9	6250	1.4	0	30.2
94962	1000	32.7	5000	1.7	150	29.3
94929	1200	31.6	6000	1.4	0	28.7
94930	1200	31.6	6000	1.4	60	28.7
94931	1200	31.6	6000	1.4	120	28.7
94932	1200	31.6	6000	1.4	180	28.7
94933	1200	31.6	6000	1.4	240	28.7
94974	950	31.0	4750	1.5	188	28.1
94936	1150	30.3	5750	1.5	57	27.3
94937	1150	30.3	5750	1.5	114	27.3
94938	1150	30.3	5750	1.5	171	27.3
94939	1150	30.3	5750	1.5	228	27.3
94940	1150	30.3	5750	1.5	285	27.3
94941	1150	30.3	5750	1.5	342	27.3
94944	1100	28.9	5500	1.5	110	25.9
94945	1100	28.9	5500	1.5	165	25.9
94946	1100	28.9	5500	1.5	220	25.9
94947	1100	28.9	5500	1.5	275	25.9
94948	1100	28.9	5500	1.5	330	25.9
94949	1100	28.9	5500	1.5	385	25.9
94953	1050	27.6	5250	1.6	156	24.4
94954	1050	27.6	5250	1.6	208	24.4
94955	1050	27.6	5250	1.6	260	24.4
94956	1050	27.6	5250	1.6	312	24.4
94957	1050	27.6	5250	1.6	364	24.4
94958	1050	27.6	5250	1.6	416	24.4
94988	900	27.6	4500	1.9	270	23.8
94963	1000	26.3	5000	1.7	200	22.9
94964	1000	26.3	5000	1.7	250	22.9
94965	1000	26.3	5000	1.7	300	22.9
94966	1000	26.3	5000	1.7	350	22.9
94967	1000	26.3	5000	1.7	400	22.9
94968	1000	26.3	5000	1.7	450	22.9
94969	1000	26.3	5000	1.7	500	22.9
94975	950	26.1	4750	1.8	235	22.5
95021	800	25.8	4000	2.1	360	21.6
94976	950	25.0	4750	1.8	282	21.4
94977	950	25.0	4750	1.8	329	21.4
94978	950	25.0	4750	1.8	376	21.4
94979	950	25.0	4750	1.8	423	21.4
94980	950	25.0	4750	1.8	470	21.4
94981	950	25.0	4750	1.8	517	21.4
95041	750	24.5	3750	2.3	407	20.0
94989	900	23.7	4500	1.9	315	19.9
94990	900	23.7	4500	1.9	360	19.9
94991	900	23.7	4500	1.9	405	19.9
94992	900	23.7	4500	1.9	450	19.9
94993	900	23.7	4500	1.9	495	19.9
94994	900	23.7	4500	1.9	540	19.9
94995	900	23.7	4500	1.9	585	19.9
95004	850	23.4	4250	2.0	336	19.4
95005	850	22.4	4250	2.0	378	18.4
95006	850	22.4	4250	2.0	420	18.4
95007	850	22.4	4250	2.0	462	18.4
95008	850	22.4	4250	2.0	504	18.4
95009	850	22.4	4250	2.0	546	18.4
95010	850	22.4	4250	2.0	588	18.4
95011	850	22.4	4250	2.0	630	18.4
95064	700	22.9	3500	2.4	455	18.0
95022	800	21.1	4000	2.1	400	16.8
95023	800	21.1	4000	2.1	440	16.8
95024	800	21.1	4000	2.1	480	16.8
95025	800	21.1	4000	2.1	520	16.8
95026	800	21.1	4000	2.1	560	16.8
95027	800	21.1	4000	2.1	600	16.8
95028	800	21.1	4000	2.1	640	16.8
95029	800	21.1	4000	2.1	680	16.8
95090	650	20.6	3250	2.6	512	15.3
95042	750	19.7	3750	2.3	444	15.2
95043	750	19.7	3750	2.3	481	15.2
95044	750	19.7	3750	2.3	518	15.2
95045	750	19.7	3750	2.3	555	15.2
95046	750	19.7	3750	2.3	592	15.2
95047	750	19.7	3750	2.3	629	15.2
95048	750	19.7	3750	2.3	666	15.2
95049	750	19.7	3750	2.3	703	15.2
95050	750	19.7	3750	2.3	740	15.2
95065	700	18.4	3500	2.4	490	13.6
95066	700	18.4	3500	2.4	525	13.6
95067	700	18.4	3500	2.4	560	13.6
95068	700	18.4	3500	2.4	595	13.6
95069	700	18.4	3500	2.4	630	13.6
95070	700	18.4	3500	2.4	665	13.6
95071	700	18.4	3500	2.4	700	13.6
95072	700	18.4	3500	2.4	735	13.6
95073	700	18.4	3500	2.4	770	13.6
95120	600	18.4	3000	2.8	570	12.7
95091	650	17.1	3250	2.6	544	11.9
95092	650	17.1	3250	2.6	576	11.9
95093	650	17.1	3250	2.6	608	11.9
95094	650	17.1	3250	2.6	640	11.9
95095	650	17.1	3250	2.6	672	11.9
95096	650	17.1	3250	2.6	704	11.9
95097	650	17.1	3250	2.6	736	11.9
95098	650	17.1	3250	2.6	768	11.9
95099	650	17.1	3250	2.6	800	11.9
95100	650	17.1	3250	2.6	832	11.9
95155	550	16.9	2750	3.1	621	10.7
95121	600	15.8	3000	2.8	600	10.1
95122	600	15.8	3000	2.8	630	10.1
95123	600	15.8	3000	2.8	660	10.1
95124	600	15.8	3000	2.8	690	10.1
95125	600	15.8	3000	2.8	720	10.1
95126	600	15.8	3000	2.8	750	10.1
95127	600	15.8	3000	2.8	780	10.1
95128	600	15.8	3000	2.8	810	10.1
95129	600	15.8	3000	2.8	840	10.1
95130	600	15.8	3000	2.8	870	10.1
95131	600	15.8	3000	2.8	900	10.1
95194	500	16.4	2500	3.4	650	9.6
95156	550	14.5	2750	3.1	648	8.3
95157	550	14.5	2750	3.1	675	8.3
95158	550	14.5	2750	3.1	702	8.3
95159	550	14.5	2750	3.1	729	8.3
95160	550	14.5	2750	3.1	756	8.3
95161	550	14.5	2750	3.1	783	8.3
95162	550	14.5	2750	3.1	810	8.3
95163	550	14.5	2750	3.1	837	8.3
95164	550	14.5	2750	3.1	864	8.3
95165	550	14.5	2750	3.1	891	8.3
95166	550	14.5	2750	3.1	918	8.3
95167	550	14.5	2750	3.1	945	8.3
95195	500	14.9	2500	3.4	675	8.1
95196	500	13.2	2500	3.4	700	6.4
95197	500	13.2	2500	3.4	725	6.4
95198	500	13.2	2500	3.4	750	6.4
95199	500	13.2	2500	3.4	775	6.4
95200	500	13.2	2500	3.4	800	6.4
95201	500	13.2	2500	3.4	825	6.4
95202	500	13.2	2500	3.4	850	6.4
95203	500	13.2	2500	3.4	875	6.4
95204	500	13.2	2500	3.4	900	6.4
95205	500	13.2	2500	3.4	925	6.4
95206	500	13.2	2500	3.4	950	6.4
95207	500	13.2	2500	3.4	975	6.4
95208	500	13.2	2500	3.4	1000	6.4

Overall score = score_ratio - 2 * repetitive DNA content