After analysis of these new predictions, 142 CDSs were added and annotated (including 49 partial genes) (supplementary table S10, Supplementary Material online).
The mitochondrial sequences were imported into the Artemis visualization and annotation tool [32], positional information of sequence features was added, and the annotated data exported in GenBank(.gb) format.
These keywords can be added and removed extremely easily by annotating a TAG to a thing.
In the four strains of N. meningitidis, from 6 to 30 new genes were added and very few of them overlap the annotated genes.
Ligand efficiencies from the ChEMBL database (32), for example, have been added to annotate protein-ligand complexes in CREDO.
A further layer of interpretation can be added by annotating the diagram with selected atom-atom distances; the reader can use the display software to added further such annotations of their own if they wish.
Figure 1 figure supplement 1 has been annotated to label major regions of ectopic expression, and an asterisk has been added to denote the DPM neurons in each panel.
Transport reactions between cytoplasm and extracellular space and between cytoplasm and organelles are poorly annotated and were added manually based on transport reactions reported in the literature.
When new data are imported, all SNPs and indels that are being added into the system are first annotated with information from refSeq (15) and dbSNP (13), as well as SIFT (16), Polyphen2 (17), PhyloP (18), LRT (19), MutationTaster (20) and GERP (21) from dbNSFP (22).
If present, the carrier substrate is added as a reactant and a product, annotated with the appropriate compartment depending on whether it is a symport or an antiport reaction.
