ATRHunter      

 

 

Experimental Results

Real-world genomic sequences

Comparison with TRF 

We analyzed three genomic sequences: yeast chromosome 1, E.coli K12 and
 E.coli O157:H7, using TRF's definition of an ATR .

Our summary results show that ATRHUNTER  produces between 35 to 70% more
ATRs than TRF, for these three genomic sequences.  The comparison uses a
variety of counting methods so that regions that have several covers by ATRs
are counted a limited number of times; the results are not sensitive to these counting methods.
To view the differences from using different counting cutoff see graph.

The detailed reports consist of all ATRs found by each program specified by
its location and an indication with * on each ATR counted in the summary
results
above.  The differential reports show which ATRs are uniquely found
by each program.

To reproduce the results of these experiments, run ATRHUNTER and TRF with the appropriate
file using the 3rd option in
ATRHUNTER submit form.

Yeast chromosome 1 ATRHUNTER's report  ,  TRF's report ,  Unique ATRs by ATRHUNTER  Unique ATRs by TRF

E.coli K12                ATRHUNTER's report  ,   TRF's report ,  Unique ATRs by ATRHUNTER  Unique ATRs by TRF

E.coli O157:H7:          ATRHUNTER's report  ,   TRF's report ,  Unique ATRs by ATRHUNTER  Unique ATRs by TRF

 

Comparison with TEIRESIAS

We analyzed the yeast chromosome 1, using TEIRESIAS's definition of an ATR.

ATRHUNTER detected about 6 times more ATRs and found all ATRs reported by TEIRESIAS.
To run this experiment use the 2nd option in ATRHUNTER submit form.

Click for the list of ATRs found by ATRHUNTER.
ATRs found by TEIRESIAS are marked with #.

 

The same genomes were analyzed with a variety of alignment parameters.
Results are reported here.
 

 

Planted ATRs in synthetic sequences

We planted 100 ATRs into 10 synthetic i.i.d. sequences of length 100,000 in
which each letter had probability 0.25 of appearing in each position, and
record the percentage of ATR recovered by ATR
HUNTER and TRF.
The average score of an ATR over all sequences was 238 and standard
deviation 116, using alignment parameters (2,-5,-7,-7). These values of the
parameters are chosen as used in Benson's paper.
The average success rate in finding the planted ATRs, using the
definition of an ATR used by TRF was 89% with a standard deviation
of 2.6% for ATR
HUNTER and 72% with a standard deviation of 4.6% for TRF.

The synthetic sequences and the lists of all planted ATRs in them are
presented along with the output of ATRHUNTER and TRF on those sequences.
(In the lists ATRs detected by
ATRHUNTER are marked with * and ATRs detected by TRF are marked with #). 

Sequence 1 with the planted ATRs   Found and missed planted ATRs 1    ATRHUNTER's output    TRF's output

Sequence 2 with the planted ATRs   Found and missed planted ATRs 2    ATRHUNTER's output    TRF's output

Sequence 3 with the planted ATRs   Found and missed planted ATRs 3    ATRHUNTER's output    TRF's output

Sequence 4 with the planted ATRs   Found and missed planted ATRs 4    ATRHUNTER's output    TRF's output

Sequence 5 with the planted ATRs   Found and missed planted ATRs 5    ATRHUNTER's output    TRF's output

Sequence 6 with the planted ATRs   Found and missed planted ATRs 6    ATRHUNTER's output    TRF's output

Sequence 7 with the planted ATRs   Found and missed planted ATRs 7    ATRHUNTER's output    TRF's output

Sequence 8 with the planted ATRs   Found and missed planted ATRs 8    ATRHUNTER's output    TRF's output

Sequence 9 with the planted ATRs   Found and missed planted ATRs 9    ATRHUNTER's output    TRF's output

Sequence 10 with the planted ATRs   Found and missed planted ATRs 10    ATRHUNTER's output    TRF's output

 

To reproduce the results of these experiments, run ATRHUNTER using the
3rd option in
ATRHUNTER submit form  and then run TRF to get the list of
ATRs detected by these programs, using any one of the above input sequences.


 

The experiment with planted ATRs has been executed for a variety of setups
and parameters values, yielding similar results. The details can be found here.

 

 

Additional experimental information shared by all experiments
 

The program automatically sets several parameters.

For an example of such set of  values see the following graph.

 

 

 Last revised December 5, 2002
Send any questions or comments to:
ywex@cs.technion.ac.il