Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign30 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (17)
Redundant probes (2)

Summary

`./analyse_probe_search_results : Mon Sep 5 11:23:33 2005`

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

Fetched probe design: ProbeDesign30
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 5
  id            : 5
  strand        : 1
  -------------

Design window length: 4157bp

All jobs for probe design are successful - total: 54
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1071 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        : 1071/1071
Putative probes exceeding selection criteria: 19/1071

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
4459	600	17.9	3000	1.3	3390	15.2
4460	600	17.9	3000	1.3	3420	15.2
4342	650	19.3	3250	2.5	3392	14.4
4590	550	16.4	2750	1.5	3375	13.5
4591	550	16.4	2750	1.5	3402	13.5
4592	550	16.4	2750	1.5	3429	13.5
4593	550	16.4	2750	1.5	3456	13.5
4594	550	16.4	2750	1.5	3483	13.5
4341	650	19.3	3250	3.2	3360	12.9
4734	500	14.9	2500	1.6	3375	11.7
4735	500	14.9	2500	1.6	3400	11.7
4736	500	14.9	2500	1.6	3425	11.7
4737	500	14.9	2500	1.6	3450	11.7
4738	500	14.9	2500	1.6	3475	11.7
4739	500	14.9	2500	1.6	3500	11.7
4740	500	14.9	2500	1.6	3525	11.7
4461	600	17.9	3000	3.2	3450	11.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
4458	600	17.9	3000	3.5	3360	10.9
4741	500	14.9	2500	3.8	3550	7.3

Overall score = score_ratio - 2 * repetitive DNA content