Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign119 - back to list

Summary
Image
Unique putative probes (29)
Putative probes (11)
Redundant probes (14)

Summary

`./analyse_probe_search_results : Wed Jun 28 17:02:22 2006`

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

Fetched probe design: ProbeDesign119
  assembly      : NCBIM36
  bias          : 3prime
  chromosome    : 7
  id            : 113
  strand        : 1
  -------------

Design window length: 2501bp

All jobs for probe design are successful - total: 35
Fetched conf : Exonerate mouse_NCBIM36 (id: 2)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 700 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            : 700/700
Putative probes that are unique                 : 29/700
Putative probes exceeding selection criteria    : 54/700 (both unique and not unique)
Putative probes with successfully-picked primers: 54/54

Identified 14 '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
106773	700	3500	-	980
106828	650	3250	-	992
106829	650	3250	-	1024
106888	600	3000	-	990
106889	600	3000	-	1020
106890	600	3000	-	1050
106891	600	3000	-	1080
106956	550	2750	-	999
106957	550	2750	-	1026
106958	550	2750	-	1053
106959	550	2750	-	1080
106960	550	2750	-	1107
106961	550	2750	-	1134
107032	500	2500	-	1000
107033	500	2500	-	1025
107034	500	2500	-	1050
107035	500	2500	-	1075
107036	500	2500	-	1100
107037	500	2500	-	1125
107038	500	2500	-	1150
107039	500	2500	-	1175
107040	500	2500	-	1200
106830	650	3250	0.6	1056
106892	600	3000	1.3	1110
106962	550	2750	1.6	1161
106774	700	3500	1.9	1015
107041	500	2500	4.6	1225
107071	500	2500	18.8	1975
107072	500	2500	18.8	2000

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
106723	750	22.1	3750	1.3	962	19.4
106827	650	19.1	3250	0.3	960	18.5
106887	600	17.6	3000	0.3	960	17.0
106955	550	16.7	2750	-	972	16.7
107031	500	15.7	2500	-	975	15.7
106772	700	20.1	3500	2.4	945	15.3
106797	650	20.6	3250	3.4	0	13.8
106722	750	21.6	3750	4.9	925	11.7
106857	600	19.0	3000	3.7	60	11.7
106954	550	15.8	2750	3.1	945	9.6
107030	500	14.4	2500	2.4	950	9.6

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
106855	600	19.0	3000	3.7	0	11.7
106856	600	19.0	3000	3.7	30	11.7
106919	550	17.4	2750	4.0	0	9.4
106920	550	17.4	2750	4.0	27	9.4
106921	550	17.4	2750	4.0	54	9.4
106922	550	17.4	2750	4.0	81	9.4
106923	550	17.4	2750	4.0	108	9.4
106992	500	15.8	2500	4.4	0	7.0
106993	500	15.8	2500	4.4	25	7.0
106994	500	15.8	2500	4.4	50	7.0
106995	500	15.8	2500	4.4	75	7.0
106996	500	15.8	2500	4.4	100	7.0
106997	500	15.8	2500	4.4	125	7.0
106998	500	15.8	2500	4.4	150	7.0

Overall score = score_ratio - 2 * repetitive DNA content