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Regular Meeting February 26, 2009. Mark Borodovsky Ivan Antonov. Topics. What have been done Results for adjacent genes using bigger gap length Results for adjacent genes using RBS site threshold Future work. What have been done. A small bug in calculating gene statistics found

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regular meeting february 26 2009

Regular MeetingFebruary 26, 2009

Mark Borodovsky

Ivan Antonov

topics
Topics
  • What have been done
  • Results for adjacent genes using bigger gap length
  • Results for adjacent genes using RBS site threshold
  • Future work

GATech

what have been done
What have been done
  • A small bug in calculating gene statistics found
  • Bigger threshold on gap length in adjacent genes is used
  • RBS site score threshold is implemented

GATech

typical genes distribution old
Typical genes distribution (old)

400 typical genes with FS

Green squares – where “All others” principle was used

End/start missing

End missing

Start missing

End/start present

1

27

15

357

Gap len >60

53

Adjacent genes

Gene overlap

114

167

190

Gap len <60

GATech

typical genes distribution new
Typical genes distribution (new)

400 typical genes with FS

Green squares – where “All others” principle was used

End/start missing

End missing

Start missing

End/start present

1

34

26

339

Gap len >60

35

Adjacent genes

Gene overlap

114

149

190

Gap len <60

GATech

slide7

Reducing number ofFalse Negatives among adjacent genesby increasing upper bound threshold on gap length

choosing upper bound threshold
Choosing upper bound threshold

Old Threshold 60

New Threshold 160

29 FS adjacent genes more

GATech

fs genes distribution
FS genes distribution

400 typical genes with FS

Green squares – where “All others” principle was used

End/start missing

End missing

Start missing

End/start present

1

34

26

339

Gap len >160

6

Adjacent genes

Gene overlap

143

149

190

Gap len <160

GATech

fsmark gm prediction
FSMark-GM prediction

GeneMark Output

Numbers of FS genes are in brackets

Adjacent Genes

Gene Overlaps

1238 (143)

366 (190)

FSMark applied

256 (145)

418 (103)

GATech

slide11

Reducing number ofFalse Positives among adjacent genesby introducing threshold on maximum value of RBS site score

fs genes distribution1
FS genes distribution

400 typical genes with FS

Green squares – where “All others” principle was used

End/start missing

End missing

Start missing

End/start present

1

34

26

339

Gap len >160

23

Adjacent genes

Gene overlap

126

149

190

Gap len <160

GATech

fsmark gm prediction1
FSMark-GM prediction

GeneMark Output

Gene Overlaps

Adjacent Genes

TP

FP

176

190

501

126

FSMark applied

111

145

131

92

GATech

conclusions
Conclusions
  • Bigger gap threshold slightly increased number of True Positives in adjacent genes
  • RBS site score threshold significantly decreased number of False positives in adjacent genes

GATech

future work
Future work
  • Try to understand why do we have so many genes with end missing
  • Take closer look at FSMark results on adjacent genes
  • What else?

GATech