Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign25 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (121)
Redundant probes (96)

Summary

`./analyse_probe_search_results : Mon Sep 5 11:47:24 2005`

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

Fetched probe design: ProbeDesign25
  assembly      : NCBIM33
  bias          : 3prime
  chromosome    : 12
  id            : 2
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 41
Fetched conf : Exonerate mouse_NCBI33 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM33/genome/masked_dusted
Fetched 405 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        : 405/405
Putative probes exceeding selection criteria: 217/405

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
424	1000	32.9	5000	-	900	32.9
425	1000	32.9	5000	-	950	32.9
426	1000	32.9	5000	-	1000	32.9
423	1000	32.9	5000	0.5	850	31.9
446	950	31.2	4750	-	893	31.2
447	950	31.2	4750	-	940	31.2
448	950	31.2	4750	-	987	31.2
449	950	31.2	4750	-	1034	31.2
469	900	29.6	4500	-	855	29.6
470	900	29.6	4500	-	900	29.6
471	900	29.6	4500	-	945	29.6
472	900	29.6	4500	-	990	29.6
473	900	29.6	4500	-	1035	29.6
445	950	31.2	4750	0.9	846	29.4
496	850	28.0	4250	-	882	28.0
497	850	28.0	4250	-	924	28.0
498	850	28.0	4250	-	966	28.0
499	850	28.0	4250	-	1008	28.0
500	850	28.0	4250	-	1050	28.0
525	800	26.3	4000	-	880	26.3
526	800	26.3	4000	-	920	26.3
527	800	26.3	4000	-	960	26.3
528	800	26.3	4000	-	1000	26.3
529	800	26.3	4000	-	1040	26.3
563	750	24.8	3750	-	1073	24.8
558	750	24.7	3750	-	888	24.7
559	750	24.7	3750	-	925	24.7
560	750	24.7	3750	-	962	24.7
561	750	24.7	3750	-	999	24.7
562	750	24.7	3750	-	1036	24.7
495	850	28.0	4250	1.8	840	24.4
557	750	24.7	3750	0.5	851	23.6
593	700	23.0	3500	-	875	23.0
594	700	23.0	3500	-	910	23.0
595	700	23.0	3500	-	945	23.0
596	700	23.0	3500	-	980	23.0
597	700	23.0	3500	-	1015	23.0
598	700	23.0	3500	-	1050	23.0
524	800	26.3	4000	1.9	840	22.6
569	700	22.4	3500	-	35	22.4
534	750	21.7	3750	-	0	21.7
633	650	21.4	3250	-	864	21.4
634	650	21.4	3250	-	896	21.4
635	650	21.4	3250	-	928	21.4
636	650	21.4	3250	-	960	21.4
637	650	21.4	3250	-	992	21.4
638	650	21.4	3250	-	1024	21.4
639	650	21.4	3250	-	1056	21.4
608	650	21.1	3250	-	64	21.1
609	650	20.7	3250	-	96	20.7
678	600	19.7	3000	-	870	19.7
679	600	19.7	3000	-	900	19.7
680	600	19.7	3000	-	930	19.7
681	600	19.7	3000	-	960	19.7
682	600	19.7	3000	-	990	19.7
683	600	19.7	3000	-	1020	19.7
684	600	19.7	3000	-	1050	19.7
653	600	19.4	3000	-	120	19.4
503	800	18.9	4000	-	0	18.9
592	700	23.0	3500	2.1	840	18.7
702	550	18.1	2750	-	162	18.1
728	550	18.1	2750	-	864	18.1
729	550	18.1	2750	-	891	18.1
730	550	18.1	2750	-	918	18.1
731	550	18.1	2750	-	945	18.1
732	550	18.1	2750	-	972	18.1
733	550	18.1	2750	-	999	18.1
734	550	18.1	2750	-	1026	18.1
735	550	18.1	2750	-	1053	18.1
535	750	17.7	3750	-	37	17.7
703	550	17.6	2750	-	189	17.6
654	600	17.3	3000	-	150	17.3
570	700	17.3	3500	-	70	17.3
793	500	16.6	2500	-	1075	16.6
571	700	16.5	3500	-	105	16.5
785	500	16.4	2500	-	875	16.4
786	500	16.4	2500	-	900	16.4
787	500	16.4	2500	-	925	16.4
788	500	16.4	2500	-	950	16.4
789	500	16.4	2500	-	975	16.4
790	500	16.4	2500	-	1000	16.4
791	500	16.4	2500	-	1025	16.4
792	500	16.4	2500	-	1050	16.4
536	750	17.7	3750	0.8	74	16.1
759	500	16.0	2500	-	225	16.0
610	650	15.3	3250	-	128	15.3
611	650	15.3	3250	-	160	15.3
677	600	19.7	3000	2.5	840	14.7
760	500	14.5	2500	-	250	14.5
784	500	16.4	2500	1.0	850	14.4
632	650	21.4	3250	3.5	832	14.3
655	600	14.2	3000	-	180	14.2
656	600	14.2	3000	-	210	14.2
704	550	13.6	2750	-	216	13.6
422	1000	20.8	5000	3.7	800	13.4
504	800	18.9	4000	2.8	40	13.4
705	550	13.0	2750	-	243	13.0
406	1000	19.7	5000	3.7	0	12.3
407	1000	19.7	5000	3.7	50	12.3
408	1000	19.7	5000	3.7	100	12.3
409	1000	19.7	5000	3.7	150	12.3
410	1000	19.7	5000	3.7	200	12.3
411	1000	19.7	5000	3.7	250	12.3
412	1000	19.7	5000	3.7	300	12.3
413	1000	19.7	5000	3.7	350	12.3
414	1000	19.7	5000	3.7	400	12.3
415	1000	19.7	5000	3.7	450	12.3
416	1000	19.7	5000	3.7	500	12.3
417	1000	19.7	5000	3.7	550	12.3
418	1000	19.7	5000	3.7	600	12.3
419	1000	19.7	5000	3.7	650	12.3
420	1000	19.7	5000	3.7	700	12.3
421	1000	19.7	5000	3.7	750	12.3
706	550	13.0	2750	0.4	270	12.2
761	500	11.8	2500	-	275	11.8
762	500	11.8	2500	-	300	11.8
727	550	18.1	2750	3.3	837	11.5
572	700	16.5	3500	3.1	140	10.2
763	500	11.8	2500	1.4	325	9.0
612	650	15.3	3250	3.7	192	7.9
657	600	14.2	3000	3.7	240	6.8

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
468	900	20.1	4500	4.1	810	11.9
444	950	19.4	4750	3.9	799	11.6
475	850	18.5	4250	3.8	0	10.9
427	950	18.7	4750	3.9	0	10.9
428	950	18.7	4750	3.9	47	10.9
429	950	18.7	4750	3.9	94	10.9
430	950	18.7	4750	3.9	141	10.9
431	950	18.7	4750	3.9	188	10.9
432	950	18.7	4750	3.9	235	10.9
433	950	18.7	4750	3.9	282	10.9
434	950	18.7	4750	3.9	329	10.9
435	950	18.7	4750	3.9	376	10.9
436	950	18.7	4750	3.9	423	10.9
437	950	18.7	4750	3.9	470	10.9
438	950	18.7	4750	3.9	517	10.9
439	950	18.7	4750	3.9	564	10.9
440	950	18.7	4750	3.9	611	10.9
441	950	18.7	4750	3.9	658	10.9
442	950	18.7	4750	3.9	705	10.9
443	950	18.7	4750	3.9	752	10.9
450	900	17.7	4500	4.1	0	9.5
451	900	17.7	4500	4.1	45	9.5
452	900	17.7	4500	4.1	90	9.5
453	900	17.7	4500	4.1	135	9.5
454	900	17.7	4500	4.1	180	9.5
455	900	17.7	4500	4.1	225	9.5
456	900	17.7	4500	4.1	270	9.5
457	900	17.7	4500	4.1	315	9.5
458	900	17.7	4500	4.1	360	9.5
459	900	17.7	4500	4.1	405	9.5
460	900	17.7	4500	4.1	450	9.5
461	900	17.7	4500	4.1	495	9.5
462	900	17.7	4500	4.1	540	9.5
463	900	17.7	4500	4.1	585	9.5
464	900	17.7	4500	4.1	630	9.5
465	900	17.7	4500	4.1	675	9.5
466	900	17.7	4500	4.1	720	9.5
467	900	17.7	4500	4.1	765	9.5
494	850	17.0	4250	4.4	798	8.3
476	850	16.7	4250	4.4	42	8.0
477	850	16.7	4250	4.4	84	8.0
478	850	16.7	4250	4.4	126	8.0
479	850	16.7	4250	4.4	168	8.0
480	850	16.7	4250	4.4	210	8.0
481	850	16.7	4250	4.4	252	8.0
482	850	16.7	4250	4.4	294	8.0
483	850	16.7	4250	4.4	336	8.0
484	850	16.7	4250	4.4	378	8.0
485	850	16.7	4250	4.4	420	8.0
486	850	16.7	4250	4.4	462	8.0
487	850	16.7	4250	4.4	504	8.0
488	850	16.7	4250	4.4	546	8.0
489	850	16.7	4250	4.4	588	8.0
490	850	16.7	4250	4.4	630	8.0
491	850	16.7	4250	4.4	672	8.0
492	850	16.7	4250	4.4	714	8.0
493	850	16.7	4250	4.4	756	8.0
523	800	16.7	4000	4.6	800	7.4
556	750	16.8	3750	4.9	814	6.9
505	800	15.7	4000	4.6	80	6.5
506	800	15.7	4000	4.6	120	6.5
507	800	15.7	4000	4.6	160	6.5
508	800	15.7	4000	4.6	200	6.5
509	800	15.7	4000	4.6	240	6.5
510	800	15.7	4000	4.6	280	6.5
511	800	15.7	4000	4.6	320	6.5
512	800	15.7	4000	4.6	360	6.5
513	800	15.7	4000	4.6	400	6.5
514	800	15.7	4000	4.6	440	6.5
515	800	15.7	4000	4.6	480	6.5
516	800	15.7	4000	4.6	520	6.5
517	800	15.7	4000	4.6	560	6.5
518	800	15.7	4000	4.6	600	6.5
519	800	15.7	4000	4.6	640	6.5
520	800	15.7	4000	4.6	680	6.5
521	800	15.7	4000	4.6	720	6.5
522	800	15.7	4000	4.6	760	6.5
537	750	14.8	3750	4.9	111	4.9
538	750	14.8	3750	4.9	148	4.9
539	750	14.8	3750	4.9	185	4.9
540	750	14.8	3750	4.9	222	4.9
541	750	14.8	3750	4.9	259	4.9
542	750	14.8	3750	4.9	296	4.9
543	750	14.8	3750	4.9	333	4.9
544	750	14.8	3750	4.9	370	4.9
545	750	14.8	3750	4.9	407	4.9
546	750	14.8	3750	4.9	444	4.9
547	750	14.8	3750	4.9	481	4.9
548	750	14.8	3750	4.9	518	4.9
549	750	14.8	3750	4.9	555	4.9
550	750	14.8	3750	4.9	592	4.9
551	750	14.8	3750	4.9	629	4.9
552	750	14.8	3750	4.9	666	4.9
553	750	14.8	3750	4.9	703	4.9
554	750	14.8	3750	4.9	740	4.9
555	750	14.8	3750	4.9	777	4.9

Overall score = score_ratio - 2 * repetitive DNA content