Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign2 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (0)
Redundant probes (0)

Summary

`./analyse_probe_search_results : Wed Mar 26 14:01:57 2008`

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

Fetched probe design: ProbeDesign2
  assembly      : NCBIM37
  chromosome    : 2
  id            : 24
  strand        : 1
  -------------

Design window length: 6327bp

All jobs for probe design are successful - total: 114
Fetched conf : Exonerate mouse_NCBIM37 (id: 2)
  Genome file(s) at: /blastdb/Mouse/NCBIM37/genome/softmasked_dusted
Fetched 2277 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
  No positional bias in selecting probes
  ------------------------

Putative probes without hits                    : 0
Putative probes with single_self_hit            : 2277/2277
Putative probes that are unique                 : 15/2277
Putative probes exceeding selection criteria    : 476/2277 (both unique and not unique)
Putative probes with successfully-picked primers: 475/476

Identified 82 'redundant' probes exceeding selection criteria
(but wholly contained by other probes, and higher repetitive DNA content)

Image

Unique (yellow), passed (green) and failed putative probes in the design window

Unique putative probes

No probes

Putative probes

No probes

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

No probes

Overall score = score_ratio - 2 * repetitive DNA content