Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign92 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (65)
Redundant probes (4)

Summary

`./analyse_probe_search_results : Wed Dec 21 12:00:21 2005`

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

Fetched probe design: ProbeDesign92
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 18
  id            : 83
  strand        : 1
  -------------

Design window length: 2668bp

All jobs for probe design are successful - total: 39
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 768 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            : 768/768
Putative probes that are unique                 : 0/768
Putative probes exceeding selection criteria    : 69/768 (both unique and not unique)
Putative probes with successfully-picked primers: 58/69

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

No probes

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
78464	850	25.9	4250	0.2	588	25.4
78509	800	24.4	4000	-	600	24.4
78510	800	24.4	4000	0.5	640	23.4
78557	750	22.9	3750	-	592	22.9
78558	750	22.9	3750	-	629	22.9
78559	750	22.9	3750	-	666	22.9
78508	800	24.4	4000	0.9	560	22.6
78610	700	21.3	3500	-	595	21.3
78611	700	21.3	3500	-	630	21.3
78612	700	21.3	3500	-	665	21.3
78613	700	21.3	3500	-	700	21.3
78614	700	21.3	3500	-	735	21.3
78463	850	25.9	4250	2.5	546	21.0
78422	900	27.4	4500	3.4	540	20.6
78668	650	19.8	3250	-	576	19.8
78669	650	19.8	3250	-	608	19.8
78670	650	19.8	3250	-	640	19.8
78671	650	19.8	3250	-	672	19.8
78672	650	19.8	3250	-	704	19.8
78673	650	19.8	3250	-	736	19.8
78674	650	19.8	3250	-	768	19.8
78556	750	22.9	3750	1.6	555	19.7
78609	700	21.3	3500	1.0	560	19.3
78560	750	22.9	3750	2.3	703	18.3
78733	600	18.3	3000	-	570	18.3
78734	600	18.3	3000	-	600	18.3
78735	600	18.3	3000	-	630	18.3
78736	600	18.3	3000	-	660	18.3
78737	600	18.3	3000	-	690	18.3
78738	600	18.3	3000	-	720	18.3
78739	600	18.3	3000	-	750	18.3
78740	600	18.3	3000	-	780	18.3
78741	600	18.3	3000	-	810	18.3
78804	550	18.0	2750	-	567	18.0
78805	550	18.0	2750	-	594	18.0
78742	600	18.3	3000	0.7	840	17.0
78806	550	16.8	2750	-	621	16.8
78807	550	16.8	2750	-	648	16.8
78808	550	16.8	2750	-	675	16.8
78809	550	16.8	2750	-	702	16.8
78810	550	16.8	2750	-	729	16.8
78811	550	16.8	2750	-	756	16.8
78812	550	16.8	2750	-	783	16.8
78813	550	16.8	2750	-	810	16.8
78814	550	16.8	2750	-	837	16.8
78815	550	16.8	2750	-	864	16.8
78887	500	16.7	2500	-	625	16.7
78888	500	16.7	2500	-	650	16.7
78885	500	16.3	2500	-	575	16.3
78886	500	16.3	2500	-	600	16.3
78675	650	19.8	3250	2.2	800	15.5
78889	500	15.2	2500	-	675	15.2
78890	500	15.2	2500	-	700	15.2
78891	500	15.2	2500	-	725	15.2
78892	500	15.2	2500	-	750	15.2
78893	500	15.2	2500	-	775	15.2
78894	500	15.2	2500	-	800	15.2
78895	500	15.2	2500	-	825	15.2
78896	500	15.2	2500	-	850	15.2
78897	500	15.2	2500	-	875	15.2
78898	500	15.2	2500	-	900	15.2
78899	500	15.2	2500	-	925	15.2
78816	550	16.8	2750	0.9	891	15.0
78884	500	16.3	2500	3.4	550	9.5
78615	700	16.9	3500	4.9	770	7.2

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
78667	650	19.8	3250	3.5	544	12.7
78732	600	19.6	3000	4.5	540	10.6
78900	500	15.2	2500	2.8	950	9.6
78803	550	18.0	2750	4.9	540	8.2

Overall score = score_ratio - 2 * repetitive DNA content