This work provides an important complement to the current annotation of the T. rubrum genome, which is currently comprised primarily of protein-coding genes.
To complement the annotation procedure based on BLAST, Blast2GO also incorporates an InterPro search functionality to add protein domain information.
Pfam [ 100] and Superfamily 1.73 [ 101] with default parameters were used to complement the annotation of the secreted proteins.
To complement the annotation from Netaffx, we used the GOAnna tool [ 51] from AgBase, a Mississippi State University curated, web-accessible resource for functional analysis of agricultural plant and animal gene products.
This collection will be a valuable resource for investigating the mechanisms and evolution of alternative splicing, and as a complement to existing annotation databases.
However, considering the hundreds of thousands of new papers published annually, an automatic annotation system with high precision and relevance can be a useful complement to manual annotation.
In addition, by identifying two additional exons of the bovine KCNIP4 gene, which are not present in the current bovine genome assembly Btau4.0, it was exemplarily demonstrated that this experimental approach is a useful complement for the annotation of the bovine genome sequence.
These results also provide important information to complement the current annotation of the T. rubrum genome, which primarily comprises protein-coding genes.
Finished Brassica rapa BAC sequences available in the public domain were annotated using the Brassica 95 k unigene set as described below and the results published to complement the other annotation tracks available through the GBrowse genome browser at.
Motivation: The interpretation of cancer-related single-nucleotide variants (SNVs) considering the protein features they affect, such as known functional sites, protein protein interfaces, or relation with already annotated mutations, might complement the annotation of genetic variants in the analysis of NGS data.
