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Finally, nine complexes were scrutinized, because a correct pose was found by at least one program but poorly ranked by all four programs.
In the BiGS dataset, all CNV calls made by all four programs were compared (Figure 1).
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But Dr. Omenn said the proposals could actually reduce the burden by establishing one set of quality measures that would be used by all six programs and perhaps by private insurers as well.
OsRUS1 and OsRUS5 were predicted to localize to the chloroplast by all six programs used.
A core set of peaks shared by all eleven programs was identified and found to comprise 75 80% of the smallest peak list for each ChIP-seq dataset (Figure 3).
RDP [42], Chimaera & MaxChi [43], [44], Bootscan [45], SiScan [46], and 3Seq [47] were also used in the Recombination Detection Program [29]; only those recombination events that were agreed upon by all six programs were retained.
Indeed, we found that if we limited our predictions to loci that are associated with terminators predicted by all three programs and predicted by QRNA [12] to encode conserved secondary structure ('ZQ' loci), 23 of the 125 (18%) experimentally confirmed loci but none of the 16 unconfirmed loci identified in our initial searches were predicted.
*Predicted to affect protein function by all three programs.
In addition, one novel variation (E177V) was also predicted as a deleterious mutation by all three programs.
Interestingly, after comparing with our previous studies [ 31] and unpublished data, we found that 17 genes were absent from the candidate lists predicted by all three programs.
We found that 113 unique miRNA:mRNA target pairs were predicted by all three programs, composed of 74 genes and 13 miRNA.
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