As such, the confidence interval provides an additional measure to help users make the decision in selecting a sample size for additional annotation and classification.
BLAST searches were carried out using Plant Expression Database (PLEXdb) [ 123] where a complete list of additional annotation for all probe sets on the wheat genome array is available.
Although these databases allow searching of SNPs according to specific criteria (e.g., chromosome location, pair-wise strain comparison, etc)., neither of them provides additional annotations for SNPs, such as deleterious/non-deleterious for missense mutations, gene expression data, or relevance to human disease.
Additional annotations for enzymes were assigned using a publicly available version (58.1) of the KEGG database [ 56].
For each mutated allele, additional annotations are also reported, i.e. annotation from HmtDB and MITOMAP resources and their occurrence among 1000 Genomes Project samples (Supplementary Information).
Additional annotations for the Affymetrix mouse 430_2 array based on probe exon mapping, signal intensity and uniqueness on the mouse genome have also been included (7).
The software expects standard VCF files as input and produces a VCF file as output which includes all variants from input files and SVM scores for each variant as additional annotations.
For example, allowing curators to view sentences that contained matches to less than the four categories typically used for searches might help identify additional annotations that can be made.
This approach maximizes the number of Arabidopsis genes with at least one experimentally based functional annotation, at the expense of adding additional annotations to genes for which some information is already known.
Although nucleomorph genes tend to be highly divergent compared with their counterparts in free-living relatives, the nucleomorph genes of C. mesostigmatica are more conservative in nature than those in the other cryptophyte nucleomorph genomes sequenced thus far, allowing for additional functional annotation of previously annotated hypothetical protein-coding genes.
