Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign88 - back to list

Summary

./analyse_probe_search_results : Tue Dec 20 11:37:44 2005

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

Fetched probe design: ProbeDesign88
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 11
  id            : 79
  strand        : 1
  -------------

Design window length: 3501bp

All jobs for probe design are successful - total: 56
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1114 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            : 1114/1114
Putative probes that are unique                 : 0/1114

  No putative probes pass with the above criteria
  Now trying: score-ratio 2, and percent repetitive 40

Putative probes exceeding selection criteria    : 58/1114 (both unique and not unique)
Putative probes with successfully-picked primers: 52/58

Identified 3 '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

No probes

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
7587750014.9250020.21375-25.5
7587850014.9250020.21400-25.5
7587950014.2250020.21425-26.2
7588050010.7250020.21450-29.7
758815008.6250020.61475-32.6
7587650014.9250024.61350-34.3
7576155016.4275027.51323-38.5
7576255016.4275027.51350-38.5
7576355015.6275027.51377-39.3
757675507.6275024.41485-41.1
7576455010.9275027.51404-44.0
758825007.1250025.61500-44.1
7587550014.9250029.61325-44.3
756646008.3300026.71470-45.0
757655509.4275027.51431-45.6
757665507.7275027.11458-46.5
757685507.6275027.11512-46.6
758835006.9250026.81525-46.7
756636008.3300027.81440-47.4
758845006.9250027.41550-47.9
7576055016.4275032.21296-48.0
7565860017.9300033.51290-49.1
7565960017.0300033.51320-50.0
7565760017.9300035.51260-53.1
756656008.3300031.21500-54.0
7566060012.9300033.51350-54.1
7587450014.9250034.61300-54.3
755696509.0325032.31408-55.6
755706509.0325032.31440-55.6
755716509.0325032.31472-55.6
754867009.7350032.71470-55.8
757695507.6275032.01539-56.4
7566160010.3300033.51380-56.7
755726509.0325033.11504-57.2
756626008.3300032.81410-57.3
7575955016.4275037.11269-57.8
7556465019.3325038.61248-57.9
758855006.9250032.41575-57.9
7556565018.5325038.61280-58.8
7556365019.3325039.51216-59.7
755686509.0325035.51376-62.1
754857009.7350036.11435-62.6
756666008.3300035.81530-63.4
756676008.3300036.01560-63.7
7540875010.4375037.21443-64.0
754837009.7350037.11365-64.6
754847009.7350037.11400-64.6
7540775010.4375037.61406-64.8
754877009.7350037.31505-64.9
7556665012.2325038.61312-65.0
7540975010.4375038.11480-65.9
757705507.6275036.91566-66.2
755676509.5325038.61344-67.8
758865006.9250037.41600-67.9
754827009.7350039.61330-69.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
7587350014.9250039.61275-64.3
755736509.0325037.21536-65.5
757715507.6275039.11593-70.6

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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