Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign22 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (12)
Redundant probes (0)

Summary

`./analyse_probe_search_results : Thu Sep 14 11:13:55 2006`

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

Fetched probe design: ProbeDesign22
  assembly      : NCBIM36
  bias          : 5prime
  chromosome    : 2
  id            : 121
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 25
Fetched conf : Exonerate mouse_NCBIM36 (id: 2)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 494 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            : 494/494
Putative probes that are unique                 : 0/494
Putative probes exceeding selection criteria    : 12/494 (both unique and not unique)
Putative probes with successfully-picked primers: 12/12

Identified 0 '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
113417	550	17.5	2750	-	540	17.5
113418	550	17.5	2750	-	567	17.5
113367	600	19.1	3000	1.2	510	16.8
113416	550	17.5	2750	0.7	513	16.1
113472	500	15.9	2500	-	525	15.9
113473	500	15.9	2500	-	550	15.9
113474	500	15.9	2500	-	575	15.9
113475	500	15.9	2500	-	600	15.9
113476	500	15.9	2500	0.2	625	15.5
113368	600	19.1	3000	2.7	540	13.8
113419	550	17.5	2750	3.6	594	10.2
113471	500	15.5	2500	3.4	500	8.7

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

No probes

Overall score = score_ratio - 2 * repetitive DNA content