Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign40 - back to list

Summary

./analyse_probe_search_results : Mon Sep 5 11:41:13 2005

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

Fetched probe design: ProbeDesign40
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : X
  id            : 16
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 28
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 557 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        : 557/557
Putative probes exceeding selection criteria: 30/557

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
1993260018.03000-123018.0
2004150016.72500-122516.7
1998455016.52750-124216.5
1998555016.52750-126916.5
1998655016.52750-129616.5
1993360018.030000.8126016.3
2004250015.42500-125015.4
2011145015.02250-127615.0
2004350015.02500-127515.0
2004450015.02500-130015.0
2004550015.02500-132515.0
2004650015.02500-135015.0
2011245014.22250-129814.2
1988665019.532502.6121614.2
1998355016.527501.3121513.9
2011345013.52250-132013.5
2011445013.52250-134213.5
2011545013.52250-136413.5
2011645013.52250-138613.5
2019140012.82000-134012.8
2011745013.522500.7140812.1
2019240012.02000-136012.0
2019340012.02000-138012.0
2019440012.02000-140012.0
2019540012.02000-142012.0
2019640012.02000-144012.0
1993160018.030003.7120010.6
1998755016.527503.313239.9
2019740012.020001.214609.5
2004750015.025004.013757.0

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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