Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign3 - back to list

Summary
Image
Unique putative probes (10)
Putative probes (125)
Redundant probes (2)

Summary

`./analyse_probe_search_results : Wed Apr 18 16:29:02 2007`

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

Fetched probe design: ProbeDesign3
  assembly      : NCBIM36
  bias          : 5prime
  chromosome    : 11
  id            : 21
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 11
Fetched conf : Exonerate mouse_NCBIM36 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 205 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            : 205/205
Putative probes that are unique                 : 10/205
Putative probes exceeding selection criteria    : 137/205 (both unique and not unique)
Putative probes with successfully-picked primers: 135/137

Identified 2 '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
23262	650	3250	-	975
23284	600	3000	-	960
23285	600	3000	-	1020
23309	550	2750	-	935
23310	550	2750	-	990
23311	550	2750	-	1045
23338	500	2500	-	950
23339	500	2500	-	1000
23340	500	2500	-	1050
23341	500	2500	-	1100

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
23155	1000	31.8	5000	-	1000	31.8
23166	950	30.3	4750	-	950	30.3
23167	950	30.3	4750	-	1045	30.3
23154	1000	29.4	5000	-	900	29.4
23179	900	28.7	4500	-	990	28.7
23180	900	28.7	4500	-	1080	28.7
23165	950	27.9	4750	-	855	27.9
23192	850	27.1	4250	-	935	27.1
23193	850	27.1	4250	-	1020	27.1
23194	850	27.1	4250	-	1105	27.1
23178	900	26.5	4500	-	900	26.5
23207	800	25.5	4000	-	960	25.5
23208	800	25.5	4000	-	1040	25.5
23209	800	25.5	4000	-	1120	25.5
23210	800	25.5	4000	-	1200	25.5
23191	850	25.0	4250	-	850	25.0
23224	750	23.9	3750	-	975	23.9
23225	750	23.9	3750	-	1050	23.9
23226	750	23.9	3750	-	1125	23.9
23227	750	23.9	3750	-	1200	23.9
23206	800	23.5	4000	-	880	23.5
23242	700	22.3	3500	-	980	22.3
23243	700	22.3	3500	-	1050	22.3
23244	700	22.3	3500	-	1120	22.3
23245	700	22.3	3500	-	1190	22.3
23246	700	22.3	3500	-	1260	22.3
23223	750	22.1	3750	-	900	22.1
23263	650	20.7	3250	-	1040	20.7
23264	650	20.7	3250	-	1105	20.7
23265	650	20.7	3250	-	1170	20.7
23266	650	20.7	3250	-	1235	20.7
23267	650	20.7	3250	-	1300	20.7
23241	700	20.6	3500	-	910	20.6
23240	700	19.8	3500	-	840	19.8
23260	650	19.1	3250	-	845	19.1
23261	650	19.1	3250	-	910	19.1
23286	600	19.1	3000	-	1080	19.1
23287	600	19.1	3000	-	1140	19.1
23288	600	19.1	3000	-	1200	19.1
23289	600	19.1	3000	-	1260	19.1
23290	600	19.1	3000	-	1320	19.1
23291	600	19.1	3000	-	1380	19.1
23283	600	17.6	3000	-	900	17.6
23312	550	17.5	2750	-	1100	17.5
23313	550	17.5	2750	-	1155	17.5
23314	550	17.5	2750	-	1210	17.5
23315	550	17.5	2750	-	1265	17.5
23316	550	17.5	2750	-	1320	17.5
23317	550	17.5	2750	-	1375	17.5
23318	550	17.5	2750	-	1430	17.5
23177	900	17.3	4500	-	810	17.3
23149	1000	16.9	5000	-	400	16.9
23150	1000	16.9	5000	-	500	16.9
23151	1000	16.9	5000	-	600	16.9
23152	1000	16.9	5000	-	700	16.9
23153	1000	16.9	5000	-	800	16.9
23282	600	16.9	3000	-	840	16.9
23222	750	16.3	3750	-	825	16.3
23308	550	16.2	2750	-	880	16.2
23160	950	16.1	4750	-	380	16.1
23161	950	16.1	4750	-	475	16.1
23162	950	16.1	4750	-	570	16.1
23163	950	16.1	4750	-	665	16.1
23164	950	16.1	4750	-	760	16.1
23342	500	15.9	2500	-	1150	15.9
23343	500	15.9	2500	-	1200	15.9
23344	500	15.9	2500	-	1250	15.9
23345	500	15.9	2500	-	1300	15.9
23346	500	15.9	2500	-	1350	15.9
23347	500	15.9	2500	-	1400	15.9
23348	500	15.9	2500	-	1450	15.9
23349	500	15.9	2500	-	1500	15.9
23172	900	15.3	4500	-	360	15.3
23173	900	15.3	4500	-	450	15.3
23174	900	15.3	4500	-	540	15.3
23175	900	15.3	4500	-	630	15.3
23176	900	15.3	4500	-	720	15.3
23336	500	14.7	2500	-	850	14.7
23337	500	14.7	2500	-	900	14.7
23185	850	14.4	4250	-	340	14.4
23186	850	14.4	4250	-	425	14.4
23187	850	14.4	4250	-	510	14.4
23188	850	14.4	4250	-	595	14.4
23189	850	14.4	4250	-	680	14.4
23190	850	14.4	4250	-	765	14.4
23200	800	13.6	4000	-	400	13.6
23201	800	13.6	4000	-	480	13.6
23202	800	13.6	4000	-	560	13.6
23203	800	13.6	4000	-	640	13.6
23204	800	13.6	4000	-	720	13.6
23205	800	13.6	4000	-	800	13.6
23199	800	13.6	4000	0.1	320	13.3
23148	1000	16.9	5000	2.1	300	12.7
23216	750	12.7	3750	-	375	12.7
23217	750	12.7	3750	-	450	12.7
23218	750	12.7	3750	-	525	12.7
23219	750	12.7	3750	-	600	12.7
23220	750	12.7	3750	-	675	12.7
23221	750	12.7	3750	-	750	12.7
23307	550	12.0	2750	-	825	12.0
23233	700	11.9	3500	-	350	11.9
23234	700	11.9	3500	-	420	11.9
23235	700	11.9	3500	-	490	11.9
23236	700	11.9	3500	-	560	11.9
23237	700	11.9	3500	-	630	11.9
23238	700	11.9	3500	-	700	11.9
23239	700	11.9	3500	-	770	11.9
23252	650	11.0	3250	-	325	11.0
23253	650	11.0	3250	-	390	11.0
23254	650	11.0	3250	-	455	11.0
23255	650	11.0	3250	-	520	11.0
23256	650	11.0	3250	-	585	11.0
23257	650	11.0	3250	-	650	11.0
23258	650	11.0	3250	-	715	11.0
23259	650	11.0	3250	-	780	11.0
23298	550	10.3	2750	-	330	10.3
23274	600	10.2	3000	-	360	10.2
23275	600	10.2	3000	-	420	10.2
23276	600	10.2	3000	-	480	10.2
23277	600	10.2	3000	-	540	10.2
23278	600	10.2	3000	-	600	10.2
23279	600	10.2	3000	-	660	10.2
23280	600	10.2	3000	-	720	10.2
23281	600	10.2	3000	-	780	10.2
23159	950	16.1	4750	3.8	285	8.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
23215	750	12.7	3750	2.8	300	7.1
23273	600	10.3	3000	3.5	300	3.3

Overall score = score_ratio - 2 * repetitive DNA content