Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign44 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (9)
Redundant probes (2)

Summary

`./analyse_probe_search_results : Wed Sep 14 17:06:15 2005`

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

Fetched probe design: ProbeDesign44
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 17
  id            : 26
  strand        : 1
  -------------

Design window length: 3001bp

All jobs for probe design are successful - total: 46
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 907 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        : 907/907
Putative probes exceeding selection criteria: 11/907

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
28097	1300	39.9	6500	4.7	1300	30.5
28126	1250	36.5	6250	4.9	1364	26.8
28338	950	31.2	4750	3.2	1269	24.9
28220	1100	31.1	5500	3.1	1265	24.9
28154	1200	29.7	6000	3.2	1260	23.2
28186	1150	26.9	5750	3.9	1254	19.0
28124	1250	24.3	6250	4.7	1240	14.9
28383	900	22.3	4500	4.3	1260	13.6
28432	850	21.0	4250	4.6	1260	11.9

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
28256	1050	21.6	5250	4.9	1248	11.9
28295	1000	21.5	5000	4.9	1250	11.7

Overall score = score_ratio - 2 * repetitive DNA content