Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign54 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (187)
Redundant probes (6)

Summary

`./analyse_probe_search_results : Mon Sep 26 11:58:27 2005`

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

Fetched probe design: ProbeDesign54
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 6
  id            : 36
  strand        : 1
  -------------

Design window length: 3001bp

All jobs for probe design are successful - total: 46
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 907 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        : 907/907
Putative probes exceeding selection criteria: 193/907

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
38802	1300	41.7	6500	-	1235	41.7
38803	1300	41.7	6500	-	1300	41.7
38804	1300	41.7	6500	-	1365	41.7
38805	1300	41.7	6500	-	1430	41.7
38806	1300	41.7	6500	-	1495	41.7
38807	1300	41.7	6500	-	1560	41.7
38808	1300	41.7	6500	-	1625	41.7
38830	1250	40.1	6250	-	1240	40.1
38831	1250	40.1	6250	-	1302	40.1
38832	1250	40.1	6250	-	1364	40.1
38833	1250	40.1	6250	-	1426	40.1
38834	1250	40.1	6250	-	1488	40.1
38835	1250	40.1	6250	-	1550	40.1
38836	1250	40.1	6250	-	1612	40.1
38860	1200	38.5	6000	-	1260	38.5
38861	1200	38.5	6000	-	1320	38.5
38862	1200	38.5	6000	-	1380	38.5
38863	1200	38.5	6000	-	1440	38.5
38864	1200	38.5	6000	-	1500	38.5
38865	1200	38.5	6000	-	1560	38.5
38866	1200	38.5	6000	-	1620	38.5
38892	1150	36.9	5750	-	1254	36.9
38893	1150	36.9	5750	-	1311	36.9
38894	1150	36.9	5750	-	1368	36.9
38895	1150	36.9	5750	-	1425	36.9
38896	1150	36.9	5750	-	1482	36.9
38897	1150	36.9	5750	-	1539	36.9
38898	1150	36.9	5750	-	1596	36.9
38859	1200	38.5	6000	0.8	1200	36.8
38801	1300	41.7	6500	3.1	1170	35.5
38925	1100	35.3	5500	-	1210	35.3
38926	1100	35.3	5500	-	1265	35.3
38927	1100	35.3	5500	-	1320	35.3
38928	1100	35.3	5500	-	1375	35.3
38929	1100	35.3	5500	-	1430	35.3
38930	1100	35.3	5500	-	1485	35.3
38931	1100	35.3	5500	-	1540	35.3
38932	1100	35.3	5500	-	1595	35.3
38829	1250	40.1	6250	2.6	1178	34.9
38891	1150	36.9	5750	1.1	1197	34.6
38962	1050	33.7	5250	-	1248	33.7
38963	1050	33.7	5250	-	1300	33.7
38964	1050	33.7	5250	-	1352	33.7
38965	1050	33.7	5250	-	1404	33.7
38966	1050	33.7	5250	-	1456	33.7
38967	1050	33.7	5250	-	1508	33.7
38968	1050	33.7	5250	-	1560	33.7
38969	1050	33.7	5250	-	1612	33.7
39001	1000	32.1	5000	-	1250	32.1
39002	1000	32.1	5000	-	1300	32.1
39003	1000	32.1	5000	-	1350	32.1
39004	1000	32.1	5000	-	1400	32.1
39005	1000	32.1	5000	-	1450	32.1
39006	1000	32.1	5000	-	1500	32.1
39007	1000	32.1	5000	-	1550	32.1
39008	1000	32.1	5000	-	1600	32.1
38961	1050	33.7	5250	1.3	1196	31.0
39043	950	30.4	4750	-	1222	30.4
39044	950	30.4	4750	-	1269	30.4
39045	950	30.4	4750	-	1316	30.4
39046	950	30.4	4750	-	1363	30.4
39047	950	30.4	4750	-	1410	30.4
39048	950	30.4	4750	-	1457	30.4
39049	950	30.4	4750	-	1504	30.4
39050	950	30.4	4750	-	1551	30.4
39051	950	30.4	4750	-	1598	30.4
39000	1000	32.1	5000	1.0	1200	30.1
39088	900	28.8	4500	-	1215	28.8
39089	900	28.8	4500	-	1260	28.8
39090	900	28.8	4500	-	1305	28.8
39091	900	28.8	4500	-	1350	28.8
39092	900	28.8	4500	-	1395	28.8
39093	900	28.8	4500	-	1440	28.8
39094	900	28.8	4500	-	1485	28.8
39095	900	28.8	4500	-	1530	28.8
39096	900	28.8	4500	-	1575	28.8
39097	900	28.8	4500	-	1620	28.8
39137	850	27.2	4250	-	1218	27.2
39138	850	27.2	4250	-	1260	27.2
39139	850	27.2	4250	-	1302	27.2
39140	850	27.2	4250	-	1344	27.2
39141	850	27.2	4250	-	1386	27.2
39142	850	27.2	4250	-	1428	27.2
39143	850	27.2	4250	-	1470	27.2
39144	850	27.2	4250	-	1512	27.2
39145	850	27.2	4250	-	1554	27.2
39146	850	27.2	4250	-	1596	27.2
39191	800	25.6	4000	-	1240	25.6
39192	800	25.6	4000	-	1280	25.6
39193	800	25.6	4000	-	1320	25.6
39194	800	25.6	4000	-	1360	25.6
39195	800	25.6	4000	-	1400	25.6
39196	800	25.6	4000	-	1440	25.6
39197	800	25.6	4000	-	1480	25.6
39198	800	25.6	4000	-	1520	25.6
39199	800	25.6	4000	-	1560	25.6
39200	800	25.6	4000	-	1600	25.6
38924	1100	35.3	5500	5.0	1155	25.3
39249	750	24.0	3750	-	1221	24.0
39250	750	24.0	3750	-	1258	24.0
39251	750	24.0	3750	-	1295	24.0
39252	750	24.0	3750	-	1332	24.0
39253	750	24.0	3750	-	1369	24.0
39254	750	24.0	3750	-	1406	24.0
39255	750	24.0	3750	-	1443	24.0
39256	750	24.0	3750	-	1480	24.0
39257	750	24.0	3750	-	1517	24.0
39258	750	24.0	3750	-	1554	24.0
39259	750	24.0	3750	-	1591	24.0
39260	750	24.0	3750	-	1628	24.0
39190	800	25.6	4000	1.2	1200	23.1
39312	700	22.4	3500	-	1225	22.4
39313	700	22.4	3500	-	1260	22.4
39314	700	22.4	3500	-	1295	22.4
39315	700	22.4	3500	-	1330	22.4
39316	700	22.4	3500	-	1365	22.4
39317	700	22.4	3500	-	1400	22.4
39318	700	22.4	3500	-	1435	22.4
39319	700	22.4	3500	-	1470	22.4
39320	700	22.4	3500	-	1505	22.4
39321	700	22.4	3500	-	1540	22.4
39322	700	22.4	3500	-	1575	22.4
39323	700	22.4	3500	-	1610	22.4
39381	650	20.8	3250	-	1216	20.8
39382	650	20.8	3250	-	1248	20.8
39383	650	20.8	3250	-	1280	20.8
39384	650	20.8	3250	-	1312	20.8
39385	650	20.8	3250	-	1344	20.8
39386	650	20.8	3250	-	1376	20.8
39387	650	20.8	3250	-	1408	20.8
39388	650	20.8	3250	-	1440	20.8
39389	650	20.8	3250	-	1472	20.8
39390	650	20.8	3250	-	1504	20.8
39391	650	20.8	3250	-	1536	20.8
39392	650	20.8	3250	-	1568	20.8
39393	650	20.8	3250	-	1600	20.8
39394	650	20.8	3250	-	1632	20.8
39458	600	19.2	3000	-	1230	19.2
39459	600	19.2	3000	-	1260	19.2
39460	600	19.2	3000	-	1290	19.2
39461	600	19.2	3000	-	1320	19.2
39462	600	19.2	3000	-	1350	19.2
39463	600	19.2	3000	-	1380	19.2
39464	600	19.2	3000	-	1410	19.2
39465	600	19.2	3000	-	1440	19.2
39466	600	19.2	3000	-	1470	19.2
39467	600	19.2	3000	-	1500	19.2
39468	600	19.2	3000	-	1530	19.2
39469	600	19.2	3000	-	1560	19.2
39470	600	19.2	3000	-	1590	19.2
39471	600	19.2	3000	-	1620	19.2
39543	550	17.6	2750	-	1215	17.6
39544	550	17.6	2750	-	1242	17.6
39545	550	17.6	2750	-	1269	17.6
39546	550	17.6	2750	-	1296	17.6
39547	550	17.6	2750	-	1323	17.6
39548	550	17.6	2750	-	1350	17.6
39549	550	17.6	2750	-	1377	17.6
39550	550	17.6	2750	-	1404	17.6
39551	550	17.6	2750	-	1431	17.6
39552	550	17.6	2750	-	1458	17.6
39553	550	17.6	2750	-	1485	17.6
39554	550	17.6	2750	-	1512	17.6
39555	550	17.6	2750	-	1539	17.6
39556	550	17.6	2750	-	1566	17.6
39557	550	17.6	2750	-	1593	17.6
39558	550	17.6	2750	-	1620	17.6
39311	700	22.4	3500	2.9	1190	16.7
39638	500	16.0	2500	-	1225	16.0
39639	500	16.0	2500	-	1250	16.0
39640	500	16.0	2500	-	1275	16.0
39641	500	16.0	2500	-	1300	16.0
39642	500	16.0	2500	-	1325	16.0
39643	500	16.0	2500	-	1350	16.0
39644	500	16.0	2500	-	1375	16.0
39645	500	16.0	2500	-	1400	16.0
39646	500	16.0	2500	-	1425	16.0
39647	500	16.0	2500	-	1450	16.0
39648	500	16.0	2500	-	1475	16.0
39649	500	16.0	2500	-	1500	16.0
39650	500	16.0	2500	-	1525	16.0
39651	500	16.0	2500	-	1550	16.0
39652	500	16.0	2500	-	1575	16.0
39653	500	16.0	2500	-	1600	16.0
39654	500	16.0	2500	-	1625	16.0
39457	600	19.2	3000	1.7	1200	15.9
39637	500	16.0	2500	2.0	1200	12.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
39042	950	30.4	4750	3.7	1175	23.1
39087	900	28.8	4500	4.4	1170	20.0
39136	850	27.2	4250	4.0	1176	19.2
39248	750	24.0	3750	3.5	1184	17.1
39380	650	20.8	3250	4.0	1184	12.8
39542	550	17.6	2750	4.0	1188	9.6

Overall score = score_ratio - 2 * repetitive DNA content