Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign58 - back to list

Summary

./analyse_probe_search_results : Thu Sep 29 17:24:04 2005

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

Fetched probe design: ProbeDesign58
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 10
  id            : 45
  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 exceeding selection criteria: 15/907

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
4706160018.530000.3168017.9
4714855017.32750-167417.3
4714955017.02750-170117.0
4715055017.02750-172817.0
4706060017.830000.7165016.4
4724450015.72500-167515.7
4724550015.72500-170015.7
4724650015.72500-172515.7
4724750015.42500-175015.4
4724850015.42500-177515.4
4714755016.327501.3164713.7
4724350014.825000.8165013.2
4698265019.232504.0163211.2
4715155016.727504.917556.8
4724950015.425004.418006.6

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).

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