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We have illustrated the capabilities of BEACON by performing comparisons of several annotations for 4 genomes.
It can display several annotations for the same region, but it cannot show several regions in a single plot.
The database provides several annotations for each SNP, including PolyPhen and PANTHER predictions of missense mutation consequence and gene expression data from Symatlas.
For comparison to a reference annotation, let us assume that for a genome sequence we generated an annotation X using one AM and we want to compare this annotation to a reference annotation, Z (note that BEACON can accept several annotations for the comparison).
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Several annotations from, for example, multiple cell lines can be supplied as multiple files or as a single file with multiple tracks.
Table S4 (Additional File 14) provides alternative SNP names arising from this work, and several annotation fields for all SNPs represented on POPA1, POPA2, POPA3, BOPA1 and BOPA2.
The software package and several annotation files for DROMPA are available on the website (http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/drompa/, see Appendix S1 in Supporting Information).
Then, several annotations and cross-references are defined for this pathway.
For example, by including the miRror 2.0 results (P-value 0.02 and the default parameters) to DAVID for annotation enrichment, several annotations stood out.
Several annotations per tissue can be made.
Several annotation methods (AMs) for eukaryotes [ 2] and prokaryotes [ 3] have been developed.
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