Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign34 - back to list

Summary

./analyse_probe_search_results : Mon Sep 5 11:30:10 2005

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

Fetched probe design: ProbeDesign34
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : X
  id            : 10
  strand        : 1
  -------------

Design window length: 3399bp

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 1120 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        : 1120/1120
Putative probes exceeding selection criteria: 155/1120

PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW
--------------------------------------------------------------

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
832380021.94000-168021.9
846570021.63500-164521.6
846670021.63500-168021.6
832280021.940000.6164020.6
839175020.53750-166520.5
839275020.53750-170220.5
854865020.13250-166420.1
854965020.13250-169620.1
855065020.13250-172820.1
825985023.242501.6163819.9
863760019.93000-165019.9
863860019.93000-168019.9
846770019.13500-171519.1
846870019.13500-175019.1
839075023.137502.3162818.6
863960018.53000-171018.5
864060018.53000-174018.5
864160018.53000-177018.5
864260018.53000-180018.5
849665018.53250-018.5
839375020.537501.1173918.4
873755018.22750-164718.2
873855018.22750-167418.2
873955018.22750-170118.2
874055018.22750-172818.2
846970019.135000.6178518.0
855165017.83250-176017.8
855265017.83250-179217.8
855365017.83250-182417.8
854765021.532502.0163217.5
858260017.03000-017.0
858360017.03000-3017.0
858460017.03000-6017.0
874155017.02750-175517.0
874255017.02750-178217.0
874355017.02750-180917.0
874455017.02750-183617.0
884850016.62500-165016.6
884950016.62500-167516.6
885050016.62500-170016.6
885150016.62500-172516.6
885250016.62500-175016.6
885350016.62500-177516.6
864360016.43000-183016.4
864460016.43000-186016.4
867655015.62750-015.6
867755015.62750-2715.6
867855015.62750-5415.6
867955015.62750-8115.6
868055015.62750-10815.6
885450015.42500-180015.4
885550015.42500-182515.4
885650015.42500-185015.4
885750015.42500-187515.4
885850015.42500-190015.4
874555015.02750-186315.0
874655015.02750-189015.0
874755015.02750-191715.0
897845015.02250-176015.0
897345014.92250-165014.9
897445014.92250-167214.9
897545014.92250-169414.9
897945014.92250-178214.9
898045014.92250-180414.9
898145014.92250-182614.9
878250014.22500-014.2
878350014.22500-2514.2
878450014.22500-5014.2
878550014.22500-7514.2
878650014.22500-10014.2
878750014.22500-12514.2
878850014.22500-15014.2
898245013.92250-184813.9
898345013.92250-187013.9
898445013.92250-189213.9
898545013.92250-191413.9
898645013.92250-193613.9
885950013.72500-192513.7
886050013.72500-195013.7
886150013.72500-197513.7
864560016.430001.5189013.4
911640013.22000-166013.2
911740013.22000-168013.2
911840013.22000-170013.2
912440013.22000-182013.2
912540013.22000-184013.2
912640013.22000-186013.2
912740013.22000-188013.2
889845012.82250-012.8
889945012.82250-2212.8
890045012.82250-4412.8
890145012.82250-6612.8
890245012.82250-8812.8
890345012.82250-11012.8
890445012.82250-13212.8
890545012.82250-15412.8
890645012.82250-17612.8
890745012.82250-19812.8
912840012.32000-190012.3
912940012.32000-192012.3
913040012.32000-194012.3
913140012.32000-196012.3
913240012.32000-198012.3
913340012.32000-200012.3
898745012.32250-195812.3
898845012.32250-198012.3
898945012.32250-200212.3
899045012.32250-202412.3
816490012.24500-012.2
832480021.940004.9172012.1
822085011.54250-011.5
822185011.54250-4211.5
863660019.930004.2162011.5
903340011.42000-011.4
903440011.42000-2011.4
903540011.42000-4011.4
903640011.42000-6011.4
903740011.42000-8011.4
903840011.42000-10011.4
903940011.42000-12011.4
904040011.42000-14011.4
904140011.42000-16011.4
904240011.42000-18011.4
904340011.42000-20011.4
904440011.42000-22011.4
904540011.42000-24011.4
904640011.42000-26011.4
913440010.92000-202010.9
913540010.92000-204010.9
913640010.92000-206010.9
913740010.92000-208010.9
828180010.94000-010.9
828280010.94000-4010.9
828380010.94000-8010.9
911540013.220001.2164010.7
874855015.027502.4194410.3
846470020.235005.0161010.2
834675010.23750-010.2
834775010.23750-3710.2
834875010.23750-7410.2
834975010.23750-11110.2
835075010.23750-14810.2
855465017.832503.8185610.1
873655018.227504.516209.1
884750016.625004.016258.6
828480010.940002.21206.4
886250013.725003.820006.1
899145012.322503.320465.6
822285011.542503.8844.0
918240011.820004.029803.8
816590012.245004.8452.7
905940011.020004.55202.0
913840010.920004.821001.4
835175010.237504.41851.4

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
897245014.922503.816287.3

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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