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Footprints : based on annotations describing DNA footprints across cell types from ENCODE.
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Generally, PCR was conducted using a forward primer (designated "WC1atg-for") designed to amplify all WC1 transcripts based on the annotations described here and an additional forward primer (designated "WC1full-forA") was used in separate reactions to preferentially amplify archetypal WC1.1 transcripts.
Such descriptions are usually based on annotations made by humans.
The remaining unmapped reads were then aligned to a spliced reference created using all possible combinations of known exons to generate putative splice junction sites based on the annotation described above.
a Observations based on annotation.
The procedures for genome assembly and annotation were based on those described in our previous studies (Chung et al. 2013; Lo, Chen, et al. 2013).
The procedures for genome sequencing, assembly, and annotation were based on those described in our previous studies (Chung et al. 2013; Lo, Chen, et al. 2013; Lo, Ku, et al. 2013).
In addition, the study's first and second authors, who were never in contact with participants and blind to diagnoses, annotated all participants' narrations based on the annotation scheme described below.
Enrichment of functional classes was tested at the level of genes, based on reftig annotation results described below, for two subsets compared to the entire annotated transcriptome: (1) all osmoregulatory candidates and (2) genes unique to each population.
Based on criteria described previously [4], a set of compounds likely to have SAR and/or other bio-annotations were downloaded from PubChem Compound.
We compute iteratively a closure of annotations which is based on the above described operation of taking acceptable hits.
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