Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign29 - back to list

Summary

./analyse_probe_search_results : Mon Sep 5 11:22:00 2005

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

Fetched probe design: ProbeDesign29
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 17
  id            : 4
  strand        : 1
  -------------

Design window length: 5190bp

All jobs for probe design are successful - total: 70
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1391 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        : 1391/1391
Putative probes exceeding selection criteria: 21/1391

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
290470021.535003.449014.6
303665019.932503.754412.6
303465019.932504.548011.0
318160018.430004.060010.4

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
303565019.932503.751212.6
317860018.430004.051010.4
317960018.430004.054010.4
318060018.430004.057010.4
317760018.930004.84809.2
333455017.527504.45138.8
333555016.927504.45408.1
333655016.927504.45678.1
333755016.927504.45948.1
333855016.927504.46218.1
333955016.927504.46488.1
351050015.725004.85756.1
351150015.325004.86005.7
351250015.325004.86255.7
351350015.325004.86505.7
351450015.325004.86755.7
351550015.325004.87005.7

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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