Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign104 - back to list

Summary

./analyse_probe_search_results : Tue Jan 31 11:12:10 2006

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

Fetched probe design: ProbeDesign104
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 13
  id            : 97
  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 5prime end of design window
  ------------------------

Putative probes without hits                    : 0
Putative probes with single_self_hit            : 907/907
Putative probes that are unique                 : 244/907
Putative probes exceeding selection criteria    : 255/907 (both unique and not unique)
Putative probes with successfully-picked primers: 255/255

Identified 7 '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
9263712506250-0
9266612006000-0
9266712006000-60
9269711505750-0
9269811505750-57
9269911505750-114
9273011005500-0
9273111005500-55
9273211005500-110
9273311005500-165
9276510505250-0
9276610505250-52
9276710505250-104
9276810505250-156
9276910505250-208
9280310005000-0
9280410005000-50
9280510005000-100
9280610005000-150
9280710005000-200
9280810005000-250
928449504750-0
928459504750-47
928469504750-94
928479504750-141
928489504750-188
928499504750-235
928509504750-282
928519504750-329
928889004500-0
928899004500-45
928909004500-90
928919004500-135
928929004500-180
928939004500-225
928949004500-270
928959004500-315
928969004500-360
929358504250-0
929368504250-42
929378504250-84
929388504250-126
929398504250-168
929408504250-210
929418504250-252
929428504250-294
929438504250-336
929448504250-378
929458504250-420
929878004000-0
929888004000-40
929898004000-80
929908004000-120
929918004000-160
929928004000-200
929938004000-240
929948004000-280
929958004000-320
929968004000-360
929978004000-400
929988004000-440
929998004000-480
930437503750-0
930447503750-37
930457503750-74
930467503750-111
930477503750-148
930487503750-185
930497503750-222
930507503750-259
930517503750-296
930527503750-333
930537503750-370
930547503750-407
930557503750-444
930567503750-481
930577503750-518
931047003500-0
931057003500-35
931067003500-70
931077003500-105
931087003500-140
931097003500-175
931107003500-210
931117003500-245
931127003500-280
931137003500-315
931147003500-350
931157003500-385
931167003500-420
931177003500-455
931187003500-490
931197003500-525
931207003500-560
931706503250-0
931716503250-32
931726503250-64
931736503250-96
931746503250-128
931756503250-160
931766503250-192
931776503250-224
931786503250-256
931796503250-288
931806503250-320
931816503250-352
931826503250-384
931836503250-416
931846503250-448
931856503250-480
931866503250-512
931876503250-544
931886503250-576
931896503250-608
932446003000-0
932456003000-30
932466003000-60
932476003000-90
932486003000-120
932496003000-150
932506003000-180
932516003000-210
932526003000-240
932536003000-270
932546003000-300
932556003000-330
932566003000-360
932576003000-390
932586003000-420
932596003000-450
932606003000-480
932616003000-510
932626003000-540
932636003000-570
932646003000-600
932656003000-630
932666003000-660
933255502750-0
933265502750-27
933275502750-54
933285502750-81
933295502750-108
933305502750-135
933315502750-162
933325502750-189
933335502750-216
933345502750-243
933355502750-270
933365502750-297
933375502750-324
933385502750-351
933395502750-378
933405502750-405
933415502750-432
933425502750-459
933435502750-486
933445502750-513
933455502750-540
933465502750-567
933475502750-594
933485502750-621
933495502750-648
933505502750-675
933515502750-702
933525502750-729
934165002500-0
934175002500-25
934185002500-50
934195002500-75
934205002500-100
934215002500-125
934225002500-150
934235002500-175
934245002500-200
934255002500-225
934265002500-250
934275002500-275
934285002500-300
934295002500-325
934305002500-350
934315002500-375
934325002500-400
934335002500-425
934345002500-450
934355002500-475
934365002500-500
934375002500-525
934385002500-550
934395002500-575
934405002500-600
934415002500-625
934425002500-650
934435002500-675
934445002500-700
934455002500-725
934465002500-750
934475002500-775
9350550025000.22225
9319065032501.1640
9326760030001.2690
92610130065001.30
92809100050001.7300
9312170035001.7595
9350450025002.02200
9344850025003.4800
9350650025005.22250
9340655027506.52187
9340755027507.32214
93507500250010.22275
93408550275012.22241
93317600300014.32190
93508500250015.22300
93318600300016.02220
93409550275017.12268
93509500250020.22325
93239650325020.92208
93319600300021.02250
93042800400021.92200
93103750375022.02220
93410550275022.02295
93168700350023.62240
93169700350023.62275
93167700350024.32205
93510500250025.22350
93240650325025.42240
93241650325025.42272
93242650325025.42304
93243650325025.42336
93320600300026.02280
93411550275026.92322
93321600300027.52310
93322600300027.52340
93323600300027.52370
93324600300027.52400
93412550275030.02349
93413550275030.02376
93414550275030.02403
93415550275030.02430
93511500250030.22375
93512500250033.02400
93513500250033.02425
93514500250033.02450
93515500250033.02475
93516500250033.02500

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
92638125033.262502.36228.6
92668120026.360003.112020.1
92700115024.757503.317118.1
9285295019.147504.537610.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
92770105028.152502.626022.9
9289790027.145002.440522.2
92734110024.155003.422017.4
9305875022.637502.955516.7
9294685022.642503.446215.8
9300080017.540004.65208.3
9335355016.127504.27567.7

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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