Given the importance of annotation environments such as ELAN [18], we note the importance of incorporating annotation results into them, since they allow the time linking of annotations to the media stream, while offering other appealing functionalities too.
By incorporating annotation information into the analysis of next-generation sequencing DNA methylation data, we provide an improvement in performance over current testing procedures.
The proposed approach is particularly useful for unreplicated data, and while we focus on the benefit of incorporating annotation using Fisher's Exact Test (FET) for unreplicated data, the extension to replicated data are straightforward (see Methods).
Original annotations of genes represented by Medicago GeneChips were updated via the SAMS software [ 60] that incorporates annotations from the Medicago genome version 3.5 [ 45].
In addition to these manually assigned terms, GOA generates high-quality GO assignments using a number of electronic methods and also incorporates annotations from a range of other GO Consortium member databases.
Future developments to the Gene Builder will add to this and incorporate annotation transfer mechanisms.
dbHiMo incorporates annotation data and analysis tools such as homology search for 603 proteomes, including the species from fungi, plants and animals.
We examined the effect of fragmentation on ORF annotation in 25 Streptomyces genomes using three different annotation types, representing different annotation targets (e.g., Pfam primarily annotates domains whereas COG and KEGG focus more on the entire protein) and sensitivities (e.g., KAAS incorporates annotation heuristics [ 15] whereas COG and Pfam annotations were based solely on RPSBLAST).
DECAFF [ 23], SWEMODE [ 24] or STM [ 25], for example, were developed to predict protein complexes [ 26] incorporating graph annotations, whereas others such as DMSP [ 27], GFA [ 28] and MATISSE [ 29] were focused on gene-expression data.
More recent developments include the Protein Family Alignment Annotation Tool (PFAAT) designed specifically for family analysis and incorporating residue annotation tools as well as integration with Jmol for protein structure display.
