Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign117 - back to list

Summary

./analyse_probe_search_results : Wed Jun 28 15:05:03 2006

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

Fetched probe design: ProbeDesign117
  assembly      : NCBIM36
  bias          : 3prime
  chromosome    : 7
  id            : 120
  strand        : 1
  -------------

Design window length: 2501bp

All jobs for probe design are successful - total: 35
Fetched conf : Exonerate mouse_NCBIM36 (id: 2)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 700 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            : 700/700
Putative probes that are unique                 : 1/700
Putative probes exceeding selection criteria    : 3/700 (both unique and not unique)
Putative probes with successfully-picked primers: 3/3

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

Chart

Unique putative probes

Putative probe IDLengthActual%rep DNADistance
1129375002500-0

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
11297150015.225002.485010.4
11293850014.025003.6256.8

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

No probes

Overall score = score_ratio - 2 * repetitive DNA content

© G2C 2014. The Genes to Cognition Programme received funding from The Wellcome Trust and the EU FP7 Framework Programmes:
EUROSPIN (FP7-HEALTH-241498), SynSys (FP7-HEALTH-242167) and GENCODYS (FP7-HEALTH-241995).

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