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To identify all sequences relevant to this analysis, the Drosophila melanogaster Hox-proteins (LAB, PB, DFD, SCR, ANTP, UBX, ABD-A and ABD-B) (see Table 1 and Appendix S1 for the seed sequences used) were used to seed iterative PSI-BLAST (version 2.2.20) [52] searches (inclusion value -h 10−5).
Each assignment is accompanied by an inclusion value of the exon with respect to the transcript under consideration.
In the regression analyses, we used the critical inclusion value for significance at the P = 0.05 level (two tailed probability) and the critical exclusion value at the P = 0.15 level.
Bootstrap and Bayesian posterior probability values are shown in Figure 2. Two major clusters were observed (New World and Old World hantavirus groups) and had a genetic distance of 28.2% (inclusion value 25%).
We have carried out a full sequence family collection with a fan-like PSI-BLAST search (inclusion value for score matrix of ≤ 0.001; e-value for PSI-blast initialization < 0.06), aligned the family and created a phylogenetic tree from hits (with the group of exonucleases represented by the structure 1Y97 as outgroup, see attachment).
In agreement, the average percent exon inclusion value (Psi), which accounts for gene expression levels, calculated using the MISO software based on RNA-Seq data for FAM204A was significantly higher in WT than in DKO cells (0.82 and 0.49, respectively; Fig. 5b ).
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Unlike almost every other dominant ethnic, racial or religious group in world history, white Protestants have ceded their socioeconomic power by hewing voluntarily to the values of merit and inclusion, values now shared broadly by Americans of different backgrounds.
Finally we selected probe sets representing genes significantly expressed at specific sites using the following inclusion values: expression ratio ≥5-fold, p value ≤0.05 to generate a TB-associated probe set list.
The threshold inclusion values for the RNA samples were >1.90 for the A260/A280 ratio and >7 for the RIN value.
A single exon intron junction can have multiple assignments of inclusion values based on the transcript under consideration.
The splice site usage value was defined as a weighted mean of the inclusion values, with the weights being the activity of the transcript under consideration.
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