Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign47 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (131)
Redundant probes (79)

Summary

`./analyse_probe_search_results : Wed Sep 21 13:54:29 2005`

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

Fetched probe design: ProbeDesign47
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 8
  id            : 29
  strand        : 1
  -------------

Design window length: 4712bp

All jobs for probe design are successful - total: 81
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1611 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        : 1611/1611
Putative probes exceeding selection criteria: 210/1611

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
30780	1150	33.2	5750	3.1	1995	27.0
30845	1100	31.8	5500	2.5	2035	26.7
30913	1050	30.3	5250	2.7	2028	25.0
30914	1050	30.3	5250	2.7	2080	25.0
30986	1000	28.9	5000	2.8	2050	23.3
30987	1000	28.9	5000	2.8	2100	23.3
30988	1000	28.9	5000	2.8	2150	23.3
30985	1000	28.9	5000	3.1	2000	22.7
30844	1100	31.8	5500	4.6	1980	22.5
31151	900	26.0	4500	2.2	2250	21.6
31063	950	27.5	4750	2.9	2021	21.6
31064	950	27.5	4750	2.9	2068	21.6
31065	950	27.5	4750	2.9	2115	21.6
31066	950	27.5	4750	2.9	2162	21.6
31067	950	27.5	4750	2.9	2209	21.6
30915	1050	30.3	5250	4.5	2132	21.4
31328	800	23.8	4000	1.4	2000	21.1
30846	1100	30.9	5500	5.0	2090	20.9
31431	750	22.3	3750	1.1	2035	20.2
31240	850	24.6	4250	2.4	2268	19.9
31241	850	24.6	4250	2.4	2310	19.9
31146	900	26.0	4500	3.1	2025	19.8
31147	900	26.0	4500	3.1	2070	19.8
31148	900	26.0	4500	3.1	2115	19.8
31149	900	26.0	4500	3.1	2160	19.8

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
31234	850	24.9	4250	3.3	2016	18.3
31235	850	24.6	4250	3.3	2058	18.0
31236	850	24.6	4250	3.3	2100	18.0
31237	850	24.6	4250	3.3	2142	18.0
31238	850	24.6	4250	3.3	2184	18.0
31239	850	24.6	4250	3.3	2226	18.0
31185	900	25.3	4500	4.2	3780	16.8
31329	800	23.8	4000	3.5	2040	16.8
31330	800	23.1	4000	3.5	2080	16.1
31331	800	23.1	4000	3.5	2120	16.1
31332	800	23.1	4000	3.5	2160	16.1
31333	800	23.1	4000	3.5	2200	16.1
31334	800	23.1	4000	3.5	2240	16.1
31276	850	23.9	4250	4.5	3780	14.9
31277	850	23.9	4250	4.5	3822	14.9
31433	750	21.9	3750	3.7	2109	14.5
31434	750	21.7	3750	3.7	2146	14.2
31435	750	21.7	3750	3.7	2183	14.2
31436	750	21.7	3750	3.7	2220	14.2
31372	800	22.5	4000	4.8	3760	13.0
31373	800	22.5	4000	4.8	3800	13.0
31374	800	22.5	4000	4.8	3840	13.0
31375	800	22.5	4000	4.8	3880	13.0
31545	700	20.8	3500	4.0	2135	12.8
31546	700	20.2	3500	4.0	2170	12.2

Overall score = score_ratio - 2 * repetitive DNA content