Argot2 (Annotation Retrieval of Genel Ontology Terms) is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate.
ANNOVAR (ANNOtation of genetic VARiants) is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides
LncADeep is an ab initio lncRNA identification and functional annotation tool based on deep learning.First, LncADeep identifies lncRNAs by integrating sequence intrinsic and homology features based on deep belief networks. Second, LncADeep predicts lncRNA-protein interactions using sequence and structure features based on deep neural networks. Third, since accurate lncRNA-protein interactions can help to infer the functions of lncRNAs.
COGNIZER is a comprehensive stand-alone framework which is enabled to simultaneously provide COG, KEGG, Pfam, GO and SEED subsystem annotations to individual sequences constituting metagenomic datasets.
Lu Q.*, Powles R.*, Wang Q., He B., and Zhao H.
Integrative tissue-specific functional annotations in the human genome provide novel insights on many complex traits and improve signal prioritization in genome wide association studies. (Submitted)
PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE), EC numbers and GO classes.