Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign94 - back to list

Summary

./analyse_probe_search_results : Wed Dec 21 12:01:52 2005

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

Fetched probe design: ProbeDesign94
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 5
  id            : 85
  strand        : 1
  -------------

Design window length: 1811bp

All jobs for probe design are successful - total: 21
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 414 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            : 414/414
Putative probes that are unique                 : 16/414
Putative probes exceeding selection criteria    : 16/414 (both unique and not unique)
Putative probes with successfully-picked primers: 16/16

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
7972460030007.5240
7972560030007.5270
7976655027508.2243
7976755027508.2270
7976855027508.2297
7976955027508.2324
7968665032508.9224
7981450025009.0250
7981550025009.0275
7981650025009.0300
7981750025009.0325
7981850025009.0350
7981950025009.0375
79813500250011.4225
79723600300012.0210
79765550275012.0216

Putative probes

No probes

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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