Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign65 - back to list

Summary
Image
Unique putative probes (108)
Putative probes (151)
Redundant probes (29)

Summary

`./analyse_probe_search_results : Fri Oct 7 10:40:22 2005`

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

Fetched probe design: ProbeDesign65
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 7
  id            : 60
  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 3prime end of design window
  ------------------------

Putative probes without hits                    : 0
Putative probes with single_self_hit            : 907/907
Putative probes that are unique                 : 108/907
Putative probes exceeding selection criteria    : 180/907 (but not unique)
Putative probes with successfully-picked primers: 280/288

Identified 29 '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
58645	900	4500	-	0
58692	850	4250	-	0
58693	850	4250	-	42
58694	850	4250	-	84
58744	800	4000	-	0
58745	800	4000	-	40
58746	800	4000	-	80
58747	800	4000	-	120
58800	750	3750	-	0
58801	750	3750	-	37
58802	750	3750	-	74
58803	750	3750	-	111
58804	750	3750	-	148
58805	750	3750	-	185
58861	700	3500	-	0
58862	700	3500	-	35
58863	700	3500	-	70
58864	700	3500	-	105
58865	700	3500	-	140
58866	700	3500	-	175
58867	700	3500	-	210
58892	700	3500	-	1085
58927	650	3250	-	0
58928	650	3250	-	32
58929	650	3250	-	64

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
58367	1300	41.7	6500	4.5	0	32.7
58368	1300	41.7	6500	4.5	65	32.7
58369	1300	41.7	6500	4.5	130	32.7
58370	1300	41.7	6500	4.5	195	32.7
58371	1300	41.7	6500	4.5	260	32.7
58372	1300	41.7	6500	4.5	325	32.7
58373	1300	41.7	6500	4.5	390	32.7
58374	1300	41.7	6500	4.5	455	32.7
58375	1300	41.7	6500	4.5	520	32.7
58376	1300	41.7	6500	4.5	585	32.7
58377	1300	41.7	6500	4.5	650	32.7
58378	1300	41.7	6500	4.5	715	32.7
58379	1300	41.7	6500	4.5	780	32.7
58582	1000	32.5	5000	-	1100	32.5
58560	1000	32.1	5000	-	0	32.1
58543	1050	34.1	5250	1.4	1092	31.2
58624	950	30.8	4750	-	1081	30.8
58625	950	30.8	4750	-	1128	30.8
58626	950	30.8	4750	-	1175	30.8
58395	1250	40.1	6250	4.6	62	30.8
58396	1250	40.1	6250	4.6	124	30.8
58397	1250	40.1	6250	4.6	186	30.8
58398	1250	40.1	6250	4.6	248	30.8
58408	1250	40.1	6250	4.6	868	30.8
58601	950	30.4	4750	-	0	30.4

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
58394	1250	40.1	6250	4.6	0	30.8
58399	1250	40.1	6250	4.6	310	30.8
58400	1250	40.1	6250	4.6	372	30.8
58401	1250	40.1	6250	4.6	434	30.8
58402	1250	40.1	6250	4.6	496	30.8
58403	1250	40.1	6250	4.6	558	30.8
58404	1250	40.1	6250	4.6	620	30.8
58405	1250	40.1	6250	4.6	682	30.8
58406	1250	40.1	6250	4.6	744	30.8
58407	1250	40.1	6250	4.6	806	30.8
58423	1200	38.5	6000	4.8	0	28.8
58424	1200	38.5	6000	4.8	60	28.8
58425	1200	38.5	6000	4.8	120	28.8
58426	1200	38.5	6000	4.8	180	28.8
58427	1200	38.5	6000	4.8	240	28.8
58428	1200	38.5	6000	4.8	300	28.8
58429	1200	38.5	6000	4.8	360	28.8
58430	1200	38.5	6000	4.8	420	28.8
58431	1200	38.5	6000	4.8	480	28.8
58432	1200	38.5	6000	4.8	540	28.8
58433	1200	38.5	6000	4.8	600	28.8
58434	1200	38.5	6000	4.8	660	28.8
58435	1200	38.5	6000	4.8	720	28.8
58436	1200	38.5	6000	4.8	780	28.8
58437	1200	38.5	6000	4.8	840	28.8

Overall score = score_ratio - 2 * repetitive DNA content