Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign36 - back to list

Summary

./analyse_probe_search_results : Mon Sep 5 11:31:44 2005

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

Fetched probe design: ProbeDesign36
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : X
  id            : 12
  strand        : 1
  -------------

Design window length: 1204bp

All jobs for probe design are successful - total: 12
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 235 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        : 235/235

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

Putative probes exceeding selection criteria: 23/235

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
112824003.620001.58000.6
112814003.620006.5780-9.4
112804003.6200011.5760-19.4
112414504.1225012.9748-21.7
112794003.6200016.5740-29.4
112404504.1225017.8726-31.5
112065004.5250021.2700-37.9
112784003.6200021.5720-39.4
112394504.1225022.7704-41.3
112055004.5250026.2675-47.9
112774003.6200026.5700-49.4
112384504.1225027.6682-51.0
111775504.8275028.7648-52.7
112045004.4250031.2650-58.0
112764003.6200031.5680-59.4
112374504.1225032.4660-60.8
111765504.1275033.6621-63.2
111526004.4300034.3600-64.3
112035003.8250036.2625-68.6
112754003.6200036.5660-69.4
112364503.7225037.3638-71.0
111755504.0275038.5594-73.1
111516003.9300039.3570-74.7

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

No probes

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).

Cookies Policy | Terms and Conditions. This site is hosted by Edinburgh University and the Genes to Cognition Programme.