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Family Pairwise Search And Cobbling - Lecture Slide - Biology 2, Slides of Biology

California State University (CSU) - ChicoBiology

True positive defined as being listed as a member of the family in the PROSITE compilation

Typology: Slides

2011/2012

Uploaded on 03/11/2012

judyth
judyth 🇺🇸

4.6

(27)

321 documents

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bg1
Comparison Protocol
Caution!
True positive defined as being listed as a
member of the family in the PROSITE
compilation
Some false positives could be actual family
members that were missed during PROSITE
compilation!
(Should be minor effect)
pf3
pf4
pf5

Partial preview of the text

Download Family Pairwise Search And Cobbling - Lecture Slide - Biology 2 and more Slides Biology in PDF only on Docsity!

Comparison Protocol

 Caution!

True positive defined as being listed as a

member of the family in the PROSITE

compilation

Some false positives could be actual family

members that were missed during PROSITE

compilation!

(Should be minor effect)

Results

BLAST FPS

BLAST

HMMER

MAST

Which is best (part 2)?

 Compare BLAST, BLAST FPS, cobbled

BLAST, cobbled BLAST FPS

 W.N. Grundy and T.L. Bailey (1999)

Family pairwise search with embedded

motif models. Bioinformatics 15: 463-

Comparison Protocol

 Evaluation metric

rank sum

 calculate difference in ROC 50 for two methods for a given family  sort by absolute value of difference  sum ranks of families for which one method is better than the other

Bigger is better!

Conclusion

 For task of finding members of a family

given a reasonable number of known

members of that family, cobbled FPS is best

currently available method!