Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign43 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (206)
Redundant probes (8)

Summary

`./analyse_probe_search_results : Tue Sep 13 14:38:24 2005`

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

Fetched probe design: ProbeDesign43
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : X
  id            : 25
  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 3prime end of design window
  ------------------------

Putative probes without hits                : 0
Putative probes with single_self_hit        : 907/907
Putative probes exceeding selection criteria: 214/907

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
27287	1150	34.6	5750	1.0	1710	32.7
27358	1050	33.2	5250	0.3	1716	32.7
27321	1100	34.8	5500	1.5	1705	31.9
27398	1000	31.6	5000	-	1750	31.6
27322	1100	33.1	5500	0.9	1760	31.3
27225	1250	31.7	6250	0.8	1736	30.1
27441	950	30.1	4750	-	1739	30.1
27442	950	30.1	4750	-	1786	30.1
27359	1050	31.6	5250	1.0	1768	29.7
27399	1000	31.6	5000	1.0	1800	29.6
27397	1000	31.6	5000	1.1	1700	29.4
27255	1200	30.5	6000	0.8	1740	28.8
27256	1200	30.5	6000	0.8	1800	28.8
27487	900	28.5	4500	-	1755	28.5
27488	900	28.5	4500	-	1800	28.5
27489	900	28.5	4500	-	1845	28.5
27486	900	28.5	4500	0.1	1710	28.3
27196	1300	33.0	6500	2.4	1690	28.2
27400	1000	30.1	5000	1.0	1850	28.1
27443	950	30.1	4750	1.1	1833	28.0
27288	1150	29.2	5750	0.9	1767	27.4
27289	1150	29.2	5750	0.9	1824	27.4
27536	850	26.9	4250	-	1722	26.9
27537	850	26.9	4250	-	1764	26.9
27538	850	26.9	4250	-	1806	26.9

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
27403	1000	25.4	5000	1.0	2000	23.4
27546	850	21.6	4250	1.2	2142	19.2
27602	800	20.3	4000	1.2	2200	17.8
27589	800	25.3	4000	3.9	1680	17.6
27712	700	22.2	3500	4.4	1680	13.3
27884	600	15.2	3000	1.7	2400	11.9
27836	600	17.5	3000	3.8	960	9.9
28076	500	12.7	2500	2.0	2500	8.7

Overall score = score_ratio - 2 * repetitive DNA content