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Peaks were required to have a S/N of 10 and have a minimum similarity score of 800 before assigning a name.
To determine valid SNPs, the minimum similarity score per polymorphic site was set at 0.75 and the minimum similarity score of all polymorphic sites at 0.8, INDEL SNPs were marked as low quality and removal of low quality at sequence ends was disabled.
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A compareACE-like [ 25] similarity metric with local cluster structures having a minimum internal similarity score of 0.8 was then used to further cluster similar intron-derived motifs from all gene clusters resulting in the final list of 26 regulatory element candidate groups [see Additional file 4].
A CompareACE-like [ 25] similarity metric with local cluster structures having a minimum internal similarity score of 0.8 was then used to further cluster similar motifs from all gene clusters resulting in the final list of 34 regulatory element candidate groups [see Additional file 3].
The parameter α, ranging from 0 to 1, determines the minimum meaningful similarity score between two diseases, and thus controls the sparsity of the phenome.
Statistical classification techniques used for recognition include those based on the minimum distance [22], similarity score [33], Kullback Leibler distance [34], maximum a posteriori (MAP) model [15, 32], maximum entropy [30], likelihood dependency test [21], support vector machine [17], and nearest neighbor classifier [10, 35].
After that, only HSPs with a minimum length of 80 bp and a similarity score of at least 80% were considered.
A match was agreed when the E-score was > 120 (optimized similarity score), with 65% sequence identity over a minimum of 30 deduced amino acid residues.
To obtain a similarity score it is sufficient to compare fingerprint bitsets, and the time to complete a similarity search depends mainly on the required minimum Tanimoto similarity.
final similarity score of Geomfinder.
Fig. 4 Validation results by minimum similarity.
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