Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign101 - back to list

Summary
Image
Unique putative probes (48)
Putative probes (9)
Redundant probes (13)

Summary

`./analyse_probe_search_results : Tue Jan 31 16:23:26 2006`

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

Fetched probe design: ProbeDesign101
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 4
  id            : 102
  strand        : 1
  -------------

Design window length: 5001bp

All jobs for probe design are successful - total: 87
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1729 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            : 1729/1729
Putative probes that are unique                 : 48/1729
Putative probes exceeding selection criteria    : 70/1729 (both unique and not unique)
Putative probes with successfully-picked primers: 70/70

Identified 13 '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
97058	500	2500	1.8	300
96681	650	3250	2.8	2656
96823	600	3000	3.0	2670
96824	600	3000	3.0	2700
96825	600	3000	3.0	2730
96980	550	2750	3.3	2673
96981	550	2750	3.3	2700
96982	550	2750	3.3	2727
96983	550	2750	3.3	2754
96984	550	2750	3.3	2781
97153	500	2500	3.6	2675
97154	500	2500	3.6	2700
97155	500	2500	3.6	2725
97156	500	2500	3.6	2750
97157	500	2500	3.6	2775
97158	500	2500	3.6	2800
97159	500	2500	3.6	2825
97059	500	2500	3.8	325
96682	650	3250	3.8	2688
97098	500	2500	6.4	1300
97057	500	2500	6.8	275
97160	500	2500	7.4	2850
96985	550	2750	8.2	2808
96891	550	2750	9.6	270
97097	500	2500	11.4	1275
96928	550	2750	14.0	1269
96927	550	2750	16.4	1242
97096	500	2500	16.4	1250
96506	700	3500	17.1	1085
96632	650	3250	18.5	1088
96633	650	3250	18.5	1120
96634	650	3250	18.5	1152
96507	700	3500	19.3	1120
96771	600	3000	20.0	1110
96772	600	3000	20.0	1140
96773	600	3000	20.0	1170
96774	600	3000	20.0	1200
96926	550	2750	21.3	1215
97095	500	2500	21.4	1225
96922	550	2750	21.8	1107
96923	550	2750	21.8	1134
96924	550	2750	21.8	1161
96925	550	2750	21.8	1188
97090	500	2500	24.0	1100
97091	500	2500	24.0	1125
97092	500	2500	24.0	1150
97093	500	2500	24.0	1175
97094	500	2500	24.0	1200

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
97152	500	16.1	2500	-	2650	16.1
96070	900	23.9	4500	4.1	315	15.7
96550	700	21.9	3500	3.3	2625	15.3
96163	850	22.6	4250	4.0	336	14.6
97151	500	15.6	2500	1.0	2625	13.6
96680	650	20.3	3250	3.7	2624	12.9
96822	600	18.8	3000	3.0	2640	12.8
96979	550	17.6	2750	3.3	2646	11.1
97126	500	13.0	2500	4.0	2000	5.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
96262	800	21.3	4000	4.2	320	12.8
96263	800	21.3	4000	4.2	360	12.8
96264	800	21.3	4000	4.2	400	12.8
96369	750	19.9	3750	4.5	333	10.9
96370	750	19.9	3750	4.5	370	10.9
96371	750	19.9	3750	4.5	407	10.9
96372	750	19.9	3750	4.5	444	10.9
96484	700	18.6	3500	4.9	315	8.9
96485	700	18.6	3500	4.9	350	8.9
96486	700	18.6	3500	4.9	385	8.9
96487	700	18.6	3500	4.9	420	8.9
96488	700	18.6	3500	4.9	455	8.9
96489	700	18.6	3500	4.9	490	8.9

Overall score = score_ratio - 2 * repetitive DNA content