Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign24 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (251)
Redundant probes (1)

Summary

`./analyse_probe_search_results : Mon Sep 5 11:45:28 2005`

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

Fetched probe design: ProbeDesign24
  assembly      : NCBIM33
  bias          : 5prime
  chromosome    : 12
  id            : 1
  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 5prime end of design window
  ------------------------

Putative probes without hits                : 0
Putative probes with single_self_hit        : 405/405
Putative probes exceeding selection criteria: 252/405

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
15	1000	32.9	5000	-	700	32.9
16	1000	32.9	5000	-	750	32.9
17	1000	32.9	5000	-	800	32.9
18	1000	32.9	5000	-	850	32.9
19	1000	32.9	5000	-	900	32.9
20	1000	32.9	5000	-	950	32.9
21	1000	32.9	5000	-	1000	32.9
37	950	31.2	4750	-	705	31.2
38	950	31.2	4750	-	752	31.2
39	950	31.2	4750	-	799	31.2
40	950	31.2	4750	-	846	31.2
41	950	31.2	4750	-	893	31.2
42	950	31.2	4750	-	940	31.2
43	950	31.2	4750	-	987	31.2
44	950	31.2	4750	-	1034	31.2
9	1000	29.9	5000	-	400	29.9
10	1000	29.9	5000	-	450	29.9
11	1000	29.9	5000	-	500	29.9
12	1000	29.9	5000	-	550	29.9
13	1000	29.9	5000	-	600	29.9
14	1000	29.9	5000	-	650	29.9
60	900	29.6	4500	-	675	29.6
61	900	29.6	4500	-	720	29.6
62	900	29.6	4500	-	765	29.6
63	900	29.6	4500	-	810	29.6

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
256	600	18.0	3000	4.7	360	8.6

Overall score = score_ratio - 2 * repetitive DNA content