Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign41 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (146)
Redundant probes (2)

Summary

`./analyse_probe_search_results : Mon Sep 5 11:43:19 2005`

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

Fetched probe design: ProbeDesign41
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : X
  id            : 17
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 28
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 557 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        : 557/557
Putative probes exceeding selection criteria: 148/557

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
20226	950	29.1	4750	-	0	29.1
20249	900	27.6	4500	-	0	27.6
20250	900	27.6	4500	-	45	27.6
20274	850	26.1	4250	-	0	26.1
20275	850	26.1	4250	-	42	26.1
20276	850	26.1	4250	-	84	26.1
20302	800	24.5	4000	-	0	24.5
20303	800	24.5	4000	-	40	24.5
20304	800	24.5	4000	-	80	24.5
20305	800	24.5	4000	-	120	24.5
20306	800	24.5	4000	-	160	24.5
20205	1000	30.7	5000	3.2	0	24.3
20277	850	26.1	4250	0.9	126	24.2
20227	950	29.1	4750	3.1	47	23.0
20333	750	23.0	3750	-	0	23.0
20334	750	23.0	3750	-	37	23.0
20335	750	23.0	3750	-	74	23.0
20336	750	23.0	3750	-	111	23.0
20337	750	23.0	3750	-	148	23.0
20338	750	23.0	3750	-	185	23.0
20251	900	27.6	4500	2.4	90	22.7
20339	750	23.0	3750	0.5	222	21.9
20367	700	21.5	3500	-	0	21.5
20368	700	21.5	3500	-	35	21.5
20369	700	21.5	3500	-	70	21.5
20370	700	21.5	3500	-	105	21.5
20371	700	21.5	3500	-	140	21.5
20372	700	21.5	3500	-	175	21.5
20373	700	21.5	3500	-	210	21.5
20374	700	21.5	3500	-	245	21.5
20405	650	19.9	3250	-	0	19.9
20406	650	19.9	3250	-	32	19.9
20407	650	19.9	3250	-	64	19.9
20408	650	19.9	3250	-	96	19.9
20409	650	19.9	3250	-	128	19.9
20410	650	19.9	3250	-	160	19.9
20411	650	19.9	3250	-	192	19.9
20412	650	19.9	3250	-	224	19.9
20413	650	19.9	3250	-	256	19.9
20414	650	19.9	3250	-	288	19.9
20415	650	19.9	3250	0.3	320	19.3
20449	600	18.4	3000	-	30	18.4
20450	600	18.4	3000	-	60	18.4
20451	600	18.4	3000	-	90	18.4
20452	600	18.4	3000	-	120	18.4
20453	600	18.4	3000	-	150	18.4
20454	600	18.4	3000	-	180	18.4
20455	600	18.4	3000	-	210	18.4
20456	600	18.4	3000	-	240	18.4
20457	600	18.4	3000	-	270	18.4
20458	600	18.4	3000	-	300	18.4
20459	600	18.4	3000	-	330	18.4
20460	600	18.4	3000	-	360	18.4
20375	700	21.5	3500	1.7	280	18.0
20497	550	18.0	2750	-	54	18.0
20498	550	16.9	2750	-	81	16.9
20499	550	16.9	2750	-	108	16.9
20500	550	16.9	2750	-	135	16.9
20501	550	16.9	2750	-	162	16.9
20502	550	16.9	2750	-	189	16.9
20503	550	16.9	2750	-	216	16.9
20504	550	16.9	2750	-	243	16.9
20505	550	16.9	2750	-	270	16.9
20506	550	16.9	2750	-	297	16.9
20507	550	16.9	2750	-	324	16.9
20508	550	16.9	2750	-	351	16.9
20509	550	16.9	2750	-	378	16.9
20510	550	16.9	2750	-	405	16.9
20546	550	16.8	2750	-	1377	16.8
20554	500	15.3	2500	-	125	15.3
20555	500	15.3	2500	-	150	15.3
20556	500	15.3	2500	-	175	15.3
20557	500	15.3	2500	-	200	15.3
20558	500	15.3	2500	-	225	15.3
20559	500	15.3	2500	-	250	15.3
20560	500	15.3	2500	-	275	15.3
20561	500	15.3	2500	-	300	15.3
20562	500	15.3	2500	-	325	15.3
20563	500	15.3	2500	-	350	15.3
20564	500	15.3	2500	-	375	15.3
20565	500	15.3	2500	-	400	15.3
20566	500	15.3	2500	-	425	15.3
20567	500	15.3	2500	-	450	15.3
20604	500	15.2	2500	-	1375	15.2
20605	500	15.2	2500	-	1400	15.2
20606	500	15.2	2500	-	1425	15.2
20617	450	14.7	2250	-	154	14.7
20252	900	24.2	4500	5.0	135	14.2
20618	450	13.8	2250	-	176	13.8
20619	450	13.8	2250	-	198	13.8
20620	450	13.8	2250	-	220	13.8
20621	450	13.8	2250	-	242	13.8
20622	450	13.8	2250	-	264	13.8
20623	450	13.8	2250	-	286	13.8
20624	450	13.8	2250	-	308	13.8
20625	450	13.8	2250	-	330	13.8
20626	450	13.8	2250	-	352	13.8
20627	450	13.8	2250	-	374	13.8
20628	450	13.8	2250	-	396	13.8
20629	450	13.8	2250	-	418	13.8
20630	450	13.8	2250	-	440	13.8
20631	450	13.8	2250	-	462	13.8
20632	450	13.8	2250	-	484	13.8
20633	450	13.8	2250	-	506	13.8
20673	450	13.7	2250	-	1386	13.7
20674	450	13.7	2250	-	1408	13.7
20675	450	13.7	2250	-	1430	13.7
20676	450	13.7	2250	-	1452	13.7
20677	450	13.7	2250	-	1474	13.7
20547	550	16.8	2750	1.8	1404	13.1
20607	500	15.2	2500	1.2	1450	12.8
20678	450	13.7	2250	0.4	1496	12.8
20568	500	15.3	2500	1.4	475	12.5
20692	400	12.3	2000	-	220	12.3
20693	400	12.3	2000	-	240	12.3
20694	400	12.3	2000	-	260	12.3
20695	400	12.3	2000	-	280	12.3
20696	400	12.3	2000	-	300	12.3
20697	400	12.3	2000	-	320	12.3
20698	400	12.3	2000	-	340	12.3
20699	400	12.3	2000	-	360	12.3
20700	400	12.3	2000	-	380	12.3
20701	400	12.3	2000	-	400	12.3
20702	400	12.3	2000	-	420	12.3
20703	400	12.3	2000	-	440	12.3
20704	400	12.3	2000	-	460	12.3
20705	400	12.3	2000	-	480	12.3
20706	400	12.3	2000	-	500	12.3
20707	400	12.3	2000	-	520	12.3
20750	400	12.2	2000	-	1380	12.2
20751	400	12.2	2000	-	1400	12.2
20752	400	12.2	2000	-	1420	12.2
20753	400	12.2	2000	-	1440	12.2
20754	400	12.2	2000	-	1460	12.2
20755	400	12.2	2000	-	1480	12.2
20756	400	12.2	2000	-	1500	12.2
20757	400	12.2	2000	-	1520	12.2
20758	400	12.2	2000	-	1540	12.2
20511	550	16.9	2750	2.5	432	11.8
20672	450	13.7	2250	1.8	1364	10.2
20634	450	13.8	2250	2.2	528	9.4
20493	600	18.3	3000	4.7	1350	9.0
20545	550	16.8	2750	4.0	1350	8.8
20603	500	15.2	2500	4.4	1350	6.4
20749	400	12.2	2000	3.0	1360	6.2
20759	400	12.2	2000	4.0	1560	4.2

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
20307	800	24.5	4000	4.0	200	16.5
20461	600	18.4	3000	3.7	390	11.1

Overall score = score_ratio - 2 * repetitive DNA content