Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign12 - back to list

Summary
Image
Unique putative probes (13)
Putative probes (19)
Redundant probes (4)

Summary

`./analyse_probe_search_results : Thu Mar 1 15:21:19 2007`

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

Fetched probe design: ProbeDesign12
  assembly      : NCBIM36
  bias          : 5prime
  chromosome    : 16
  id            : 12
  strand        : 1
  -------------

Design window length: 647bp

All jobs for probe design are successful - total: 15
Fetched conf : Exonerate mouse_NCBIM36 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 287 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            : 287/287
Putative probes that are unique                 : 13/287
Putative probes exceeding selection criteria    : 36/287 (both unique and not unique)
Putative probes with successfully-picked primers: 36/36

Identified 4 '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
9035	350	1750	-	34
9136	250	1250	-	132
9139	250	1250	-	168
9174	225	1125	-	165
9175	225	1125	-	176
9176	225	1125	-	187
9215	200	1000	-	170
9216	200	1000	-	180
9217	200	1000	-	190
9218	200	1000	-	200
9219	200	1000	-	210
9220	200	1000	-	220
9198	200	1000	7.5	0

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
9005	400	13.2	2000	-	20	13.2
9018	375	12.3	1875	-	18	12.3
9019	375	12.3	1875	-	36	12.3
9020	375	11.9	1875	-	54	11.9
9034	350	11.5	1750	-	17	11.5
9036	350	11.5	1750	-	51	11.5
9037	350	11.5	1750	-	68	11.5
9052	325	10.7	1625	-	16	10.7
9053	325	10.7	1625	-	32	10.7
9054	325	10.7	1625	-	48	10.7
9055	325	10.7	1625	-	64	10.7
9056	325	10.7	1625	-	80	10.7
9057	325	10.7	1625	-	96	10.7
9038	350	11.1	1750	0.9	85	9.4
9006	400	12.7	2000	2.0	40	8.7
9058	325	10.4	1625	1.5	112	7.3
8994	425	13.5	2125	3.3	21	6.9
8993	425	14.0	2125	3.5	0	6.9
9021	375	11.9	1875	4.0	72	3.9

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Overall
9004	400	13.2	2000	3.8	5.7
9017	375	12.3	1875	4.0	4.3
9033	350	11.5	1750	4.3	2.9
9051	325	10.7	1625	4.6	1.5

Overall score = score_ratio - 2 * repetitive DNA content