Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign97 - back to list

Summary

./analyse_probe_search_results : Wed Dec 21 12:04:07 2005

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

Fetched probe design: ProbeDesign97
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 14
  id            : 88
  strand        : 1
  -------------

Design window length: 4001bp

All jobs for probe design are successful - total: 66
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1318 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            : 1318/1318
Putative probes that are unique                 : 52/1318
Putative probes exceeding selection criteria    : 155/1318 (both unique and not unique)
Putative probes with successfully-picked primers: 155/155

Identified 5 '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
817637003500-1785
817647003500-1820
818636503250-1792
818646503250-1824
818656503250-1856
819726003000-1800
819736003000-1830
819746003000-1860
819756003000-1890
819766003000-1920
820935502750-1809
820945502750-1836
820955502750-1863
820965502750-1890
820975502750-1917
820985502750-1944
822265002500-1800
822275002500-1825
822285002500-1850
822295002500-1875
822305002500-1900
822315002500-1925
822325002500-1950
822335002500-1975
822345002500-2000
8209955027500.21971
8223550025001.02025
8227650025001.03050
8201060030002.22940
8213555027502.42943
8213655027502.42970
8213755027502.42997
8227250025002.62950
8227350025002.62975
8227450025002.63000
8227550025002.63025
8227150025002.82925
8189865032504.22912
8213455027504.22916
8200960030004.82910
8227050025007.82900
8189765032509.12880
8213355027509.12889
8200860030009.82880
82269500250012.82875
81896650325014.02848
82132550275014.02862
82007600300014.82850
81793700350014.92835
82268500250017.82850
82131550275018.92835
82267500250022.82825

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
8143390029.84500-157529.8
8143490029.84500-162029.8
8136695031.547501.6155128.3
8150585028.14250-159628.1
8150685028.14250-163828.1
8158380026.54000-160026.5
8158480026.54000-164026.5
8158580026.54000-168026.5
8158680026.54000-172026.5
8150485028.142501.4155425.3
8150785026.942500.9168025.0
8158280026.540000.8156025.0
8166775024.83750-159124.8
8166875024.83750-162824.8
8166975024.83750-166524.8
8167075024.83750-170224.8
8167175024.83750-173924.8
8136795028.347502.4159823.4
8167275024.837500.8177623.2
8175770023.23500-157523.2
8175870023.23500-161023.2
8175970023.23500-164523.2
8176070023.23500-168023.2
8176170023.23500-171523.2
8176270023.23500-175023.2
8166675024.837501.6155421.6
8185665021.53250-156821.5
8185765021.53250-160021.5
8185865021.53250-163221.5
8185965021.53250-166421.5
8186065021.53250-169621.5
8186165021.53250-172821.5
8186265021.53250-176021.5
81303100028.150004.1155019.9
8196560019.93000-159019.9
8196660019.93000-162019.9
8196760019.93000-165019.9
8196860019.93000-168019.9
8196960019.93000-171019.9
8197060019.93000-174019.9
8197160019.93000-177019.9
8170375023.937502.1292319.6
8201460019.13000-306019.1
8201560019.13000-309019.1
8170475023.937502.4296019.1
8179670022.335001.9294018.6
8179770022.335001.9297518.6
8208455018.22750-156618.2
8208555018.22750-159318.2
8208655018.22750-162018.2
8208755018.22750-164718.2
8208855018.22750-167418.2
8208955018.22750-170118.2
8209055018.22750-172818.2
8209155018.22750-175518.2
8209255018.22750-178218.2
8196460019.930001.0156017.9
8214055017.52750-307817.5
8214155017.52750-310517.5
8214255017.52750-313217.5
8179870022.335002.6301017.2
8161680025.540004.2292017.0
8189965020.732502.0294416.7
8190065020.732502.0297616.7
8190165020.732502.0300816.7
8190265020.732502.0304016.7
8143290024.645004.0153016.6
8186665020.632502.0188816.6
8221750016.62500-157516.6
8221850016.62500-160016.6
8221950016.62500-162516.6
8222050016.62500-165016.6
8222150016.62500-167516.6
8222250016.62500-170016.6
8222350016.62500-172516.6
8222450016.62500-175016.6
8222550016.62500-177516.6
8213955017.527500.7305116.1
8214355017.527500.7315916.1
8227750015.92500-307515.9
8227850015.92500-310015.9
8227950015.92500-312515.9
8228050015.92500-315015.9
8228150015.92500-317515.9
8228250015.92500-320015.9
8190365020.732502.6307215.5
8201160019.130002.2297014.8
8201260019.130002.2300014.8
8201360019.130002.2303014.8
8201660019.130002.5312014.1
8213855017.527502.4302412.8
8179570022.335004.9290512.6
8175670019.135003.7154011.7
8221650016.625003.2155010.2
8143590018.445004.416659.6
8158780018.340004.417609.5
8176570017.235004.318558.7
8228350015.925004.032257.9

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
8185565017.832504.615368.5
8197760016.930004.219508.5
8210055016.427504.219988.0
8208355015.027504.915395.2
8223650014.025005.020504.0

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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