Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign32 - back to list

Summary

./analyse_probe_search_results : Mon Sep 5 11:27:03 2005

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

Fetched probe design: ProbeDesign32
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : X
  id            : 7
  strand        : 1
  -------------

Design window length: 2432bp

All jobs for probe design are successful - total: 27
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 537 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        : 537/537

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

Putative probes exceeding selection criteria: 34/537

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
656750010.9250025.2825-39.5
65665009.1250025.2800-41.3
65685007.8250025.2850-42.6
65695005.8250025.2875-44.6
65705004.7250025.2900-45.7
65655006.4250030.0775-53.6
65715003.9250029.6925-55.3
64935508.6275032.0783-55.4
65645005.7250030.6750-55.5
64945507.6275032.0810-56.4
64925506.4275032.0756-57.6
64955505.7275032.0837-58.3
64965504.7275032.0864-59.3
64975503.8275032.0891-60.2
64915505.8275035.6729-65.4
65635005.3250035.6725-65.9
65725003.3250034.6950-65.9
64985503.3275034.7918-66.2
61109507.6475037.6282-67.5
608110008.0500038.0300-68.0
64905505.2275036.7702-68.2
64276006.8300037.7750-68.5
64286006.7300037.7780-68.6
608010008.0500038.5250-69.0
64266006.1300037.7720-69.2
64296005.3300037.7810-70.1
64306004.2300037.7840-71.2
64316003.5300037.7870-71.8
64326003.0300037.7900-72.3

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
61439007.2450039.7315-72.1
61119507.6475039.9329-72.2
64256005.6300039.2690-72.7
65735002.9250039.6975-76.3
64995502.8275039.6945-76.5

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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