Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign43 - back to list

Summary

./analyse_probe_search_results : Tue Sep 13 14:38:24 2005

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

Fetched probe design: ProbeDesign43
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : X
  id            : 25
  strand        : 1
  -------------

Design window length: 3001bp

All jobs for probe design are successful - total: 46
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 907 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        : 907/907
Putative probes exceeding selection criteria: 214/907

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
27287115034.657501.0171032.7
27358105033.252500.3171632.7
27321110034.855001.5170531.9
27398100031.65000-175031.6
27322110033.155000.9176031.3
27225125031.762500.8173630.1
2744195030.14750-173930.1
2744295030.14750-178630.1
27359105031.652501.0176829.7
27399100031.650001.0180029.6
27397100031.650001.1170029.4
27255120030.560000.8174028.8
27256120030.560000.8180028.8
2748790028.54500-175528.5
2748890028.54500-180028.5
2748990028.54500-184528.5
2748690028.545000.1171028.3
27196130033.065002.4169028.2
27400100030.150001.0185028.1
2744395030.147501.1183328.0
27288115029.257500.9176727.4
27289115029.257500.9182427.4
2753685026.94250-172226.9
2753785026.94250-176426.9
2753885026.94250-180626.9
2753985026.94250-184826.9
2754085026.94250-189026.9
2744495028.647501.1188026.5
2749090028.545001.1189026.3
27323110027.955000.9181526.1
27324110027.955000.9187026.1
2744095030.147502.0169226.1
2759080025.34000-172025.3
2759180025.34000-176025.3
2759280025.34000-180025.3
2759380025.34000-184025.3
2759480025.34000-188025.3
2759580025.34000-192025.3
2759680025.34000-196025.3
2749190027.145001.1193524.9
27360105026.652501.0182024.7
27361105026.652501.0187224.7
27362105026.652501.0192424.7
2754185026.942501.2193224.5
27357105033.252504.5166424.3
27224125031.762503.8167424.2
2765075023.73750-173923.7
2765175023.73750-177623.7
2765275023.73750-181323.7
2765375023.73750-185023.7
2765475023.73750-188723.7
2765575023.73750-192423.7
2765675023.73750-196123.7
2765775023.73750-199823.7
27254120030.560003.4168023.6
27401100025.450001.0190023.4
27402100025.450001.0195023.4
2754285025.642501.2197423.2
2754385025.642501.2201623.2
2759780025.340001.2200022.8
2771370022.23500-171522.2
2771470022.23500-175022.2
2771570022.23500-178522.2
2771670022.23500-182022.2
2771770022.23500-185522.2
2771870022.23500-189022.2
2771970022.23500-192522.2
2772070022.23500-196022.2
2772170022.23500-199522.2
2772270022.23500-203022.2
2744595024.147501.1192722.0
2744695024.147501.1197422.0
2744795024.147501.1202122.0
2759880024.140001.2204021.6
2772370022.235000.3206521.6
2764975023.737501.2170221.3
2765875023.737501.3203521.1
2749290022.845001.1198020.6
2749390022.845001.1202520.6
2749490022.845001.1207020.6
2778465020.63250-172820.6
2778565020.63250-176020.6
2778665020.63250-179220.6
2778765020.63250-182420.6
2778865020.63250-185620.6
2778965020.63250-188820.6
2779065020.63250-192020.6
2779165020.63250-195220.6
2779265020.63250-198420.6
2779365020.63250-201620.6
2779465020.63250-204820.6
2779565020.63250-208020.6
2779665020.63250-211220.6
2765975022.637501.3207219.9
2766075022.637501.3210919.9
2753585026.942503.6168019.6
2786260019.53000-174019.5
2772470022.235001.4210019.3
2754485021.642501.2205819.2
2754585021.642501.2210019.2
2786360019.03000-177019.0
2786460019.03000-180019.0
2786560019.03000-183019.0
2786660019.03000-186019.0
2786760019.03000-189019.0
2786860019.03000-192019.0
2786960019.03000-195019.0
2787060019.03000-198019.0
2787160019.03000-201019.0
2787260019.03000-204019.0
2787360019.03000-207019.0
2787460019.03000-210019.0
2787560019.03000-213019.0
2787660019.03000-216019.0
2772570021.135001.4213518.2
2759980020.340001.2208017.8
2760080020.340001.2212017.8
2760180020.340001.2216017.8
2779765020.632501.5214417.5
2795255017.42750-180917.4
2795355017.42750-183617.4
2795455017.42750-186317.4
2795555017.42750-189017.4
2795655017.42750-191717.4
2795755017.42750-194417.4
2795855017.42750-197117.4
2795955017.42750-199817.4
2796055017.42750-202517.4
2796155017.42750-205217.4
2796255017.42750-207917.4
2796355017.42750-210617.4
2796455017.42750-213317.4
2796555017.42750-216017.4
2796655017.42750-218717.4
2796755017.427500.2221417.0
2779865019.632501.5217616.5
2779965019.632501.5220816.5
2766175019.037501.3214616.4
2766275019.037501.3218316.4
2766375019.037501.3222016.4
2778365020.732502.3169616.1
2805050015.82500-185015.8
2805150015.82500-187515.8
2805250015.82500-190015.8
2805350015.82500-192515.8
2805450015.82500-195015.8
2805550015.82500-197515.8
2805650015.82500-200015.8
2805750015.82500-202515.8
2805850015.82500-205015.8
2805950015.82500-207515.8
2806050015.82500-210015.8
2806150015.82500-212515.8
2806250015.82500-215015.8
2806350015.82500-217515.8
2806450015.82500-220015.8
2806550015.82500-222515.8
2806650015.82500-225015.8
2787760019.030001.7219015.7
2772670017.835001.4217014.9
2772770017.835001.4220514.9
2772870017.835001.4224014.9
2772970017.835001.4227514.9
2787860018.130001.7222014.7
2787960018.130001.7225014.7
2783760017.530001.799014.2
2783860017.530001.7102014.2
2796855017.427501.8224113.8
2780065016.532501.5224013.4
2780165016.532501.5227213.4
2780265016.532501.5230413.4
2780365016.532501.5233613.4
2796955016.627501.8226812.9
2797055016.627501.8229512.9
2792255016.127501.899912.4
2792355016.127501.8102612.4
2792455016.127501.8105312.4
2806850016.225002.0230012.2
2776065019.032503.596011.9
2788060015.230001.7228011.9
2788160015.230001.7231011.9
2788260015.230001.7234011.9
2788360015.230001.7237011.9
2801550014.625001.497511.8
2806950015.125002.0232511.1
2807050015.125002.0235011.1
2801650014.625002.0100010.6
2801750014.625002.0102510.6
2801850014.625002.0105010.6
2801950014.625002.0107510.6
2802050014.625002.0110010.6
2797155014.027501.8232210.3
2797255014.027501.8234910.3
2797355014.027501.8237610.3
2797455014.027501.8240310.3
2797555014.027501.8243010.3
2776165019.032504.69929.8
2792555016.127503.310809.5
2802150014.625002.611259.4
2792155016.127503.59729.2
2807150012.725002.023758.7
2807250012.725002.024008.7
2807350012.725002.024258.7
2807450012.725002.024508.7
2807550012.725002.024758.7
2801450014.625004.69505.4

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
27403100025.450001.0200023.4
2754685021.642501.2214219.2
2760280020.340001.2220017.8
2758980025.340003.9168017.6
2771270022.235004.4168013.3
2788460015.230001.7240011.9
2783660017.530003.89609.9
2807650012.725002.025008.7

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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