title: Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences.
abstract: Functional annotation of the gigantic metagenomic data is one of the major time-consuming and computationally demanding tasks, which is currently a bottleneck for the efficient analysis. The commonly used homology-based methods to functionally annotate and classify proteins are extremely slow. Therefore, to achieve faster and accurate functional annotation, we have developed an orthology-based functional classifier 'Woods' by using a combination of machine learning and similarity-based approaches. Woods displayed a precision of 98.79% on independent genomic dataset, 96.66% on simulated metagenomic dataset and >97% on two real metagenomic datasets. In addition, it performed >87 times faster than BLAST on the two real metagenomic datasets. Woods can be used as a highly efficient and accurate classifier with high-throughput capability which facilitates its usability on large metagenomic datasets.
authors: MetaInformatics Laboratory, Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India. Electronic address: ashoks@iiserb.ac.in.
authors: Ashok K
authors: AK
authors: Sharma
authors: MetaInformatics Laboratory, Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India. Electronic address: ankitg@iiserb.ac.in.
authors: Ankit
authors: A
authors: Gupta
authors: MetaInformatics Laboratory, Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India. Electronic address: drsanjivk@gmail.com.
authors: Sanjiv
authors: S
authors: Kumar
authors: MetaInformatics Laboratory, Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India. Electronic address: darshan@iiserb.ac.in.
authors: Darshan B
authors: DB
authors: Dhakan
authors: MetaInformatics Laboratory, Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India. Electronic address: vineetks@iiserb.ac.in.
authors: Vineet K
authors: VK
authors: Sharma
mesh_terms: D023281:Genomics / Q000379:methods*; D006801:Humans; D000069550:Machine Learning; D056186:Metagenomics / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins
keywords: Functional annotation; Machine learning; Metagenome; Random Forest