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The Project is AcidMiner: but what is that?

How did it go

Project Results

Technical Observations and Lessons

Lessons and Conclusion

Question and Answers

What is AcidMiner

How did it go

Project Results

Technical Observations and Lessons

Lessons and Conclusion

Q&A

Quick Ref Blob:Genome is the entire set of genes

(and everything in between)

in an organism;Evolutionarily family tree of species is

called a phylogeny.

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Quick Ref Blob:Proteins are made out of 20 kinds of

monomers called amino acids;

Evolutionarily related proteins are called homologs;Most evolutionary changes occur by amino acid

substitutions (1 at a time).

L

I

L

I

L

L

I

I

LI

IL

OR

L

I

L

L

I

I

LI

IL

OR

L

L

IL

Outgroup

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Genome-wide

phylogenetic

reconstruction of amino

acid substitutions using

triplets of genomes is

routine, but using the

whole phylogenyinformation is not trivial

What is AcidMiner

How did it go

Technical Observations and Lessons

Project Results

Lessons and Conclusion

Q&A

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Onlinedatabase at

Indiana State

University

OtherSources

Manual Feed

Java Code

CachDMBS

JDBC/ODBC

SQL

Results

???

StatisticalSoftware

TableswithAggregates

???

What is AcidMiner

How did it go

Project Results

Technical Observations and Lessons

Lessons and Conclusion

Q&A

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Onlinedatabase at

Indiana State

University

OtherSources

Java Code

GeneOntology,etc

Manual Feed

Results

Excel(Oops)

TableswithAggregates

CachDMBS

DBVisualizer(SQL)

Export to Flat

Files (CSV,XLS)

SQL(DBVisualizer)

StatisticalSoftware

(JMP)

Manual

Semi-Automatic

data Retrieval

In-DatabaseCalculations

(DerivativeProcessing)

Results: Fluxes in Amino acid substitutions

Frequencies are far from an

equilibrium: frequent aminoacids are losers, rare are

gainers (so frequencies are ontheir way to an equilibrium)

Consistent with Jordan et al.,Nature 2005.

Most proteins lose average

polarity compared to the

ancestral state. This effect isthe strongest in intracellular,

and the weakest in membraneproteins.

Rela

tive

loss

/gai n

Project Results Project Results

Remaining copy

conserved

One copy conserved,

the other underpositive selection

Both copiesconserved

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Project Results

Yes, in most functional classes (except transporters)

Project Results

Yes, in numerous gene families, indicating widespread

neofunctionalization.

Caveat: some may be a signature of retained pseudogene.

Asymmetryparameter

Number ofduplications

tested

Clade asymmetry,FDR = 0.05

Clade asymmetry,Bonferroni-

adjusted P< 0.05

Number ofsubstitutions

4646 1770 905

|DPolarity| 2951 179 39

What is AcidMiner

How did it go

Project Results

Technical Observations and Lessons

Lessons and Conclusion

Q&A

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What is AcidMiner

How did it go

Project Results

Technical Observations and Lessons

Lessons and Conclusion

Q&A

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What is AcidMiner

How did it go

Technical Observations and Lessons

Project Results

Lessons and Conclusion

Q&A