Literature DB >> 25863333

Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences.

Ashok K Sharma1, Ankit Gupta2, Sanjiv Kumar3, Darshan B Dhakan4, Vineet K Sharma5.   

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.
Copyright © 2015. Published by Elsevier Inc.

Keywords:  Functional annotation; Machine learning; Metagenome; Random Forest

Mesh:

Substances:

Year:  2015        PMID: 25863333     DOI: 10.1016/j.ygeno.2015.04.001

Source DB:  PubMed          Journal:  Genomics        ISSN: 0888-7543            Impact factor:   5.736


  15 in total

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Authors:  Marcus J Claesson; Adam G Clooney; Paul W O'Toole
Journal:  Nat Rev Gastroenterol Hepatol       Date:  2017-08-09       Impact factor: 46.802

2.  Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species.

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Review 3.  Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.

Authors:  Bilal Wajid; Faria Anwar; Imran Wajid; Haseeb Nisar; Sharoze Meraj; Ali Zafar; Mustafa Kamal Al-Shawaqfeh; Ali Riza Ekti; Asia Khatoon; Jan S Suchodolski
Journal:  Funct Integr Genomics       Date:  2021-10-18       Impact factor: 3.410

4.  ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins.

Authors:  Sudheer Gupta; Midhun K Madhu; Ashok K Sharma; Vineet K Sharma
Journal:  J Transl Med       Date:  2016-06-14       Impact factor: 5.531

5.  Prediction of anti-inflammatory proteins/peptides: an insilico approach.

Authors:  Sudheer Gupta; Ashok K Sharma; Vibhuti Shastri; Midhun K Madhu; Vineet K Sharma
Journal:  J Transl Med       Date:  2017-01-06       Impact factor: 5.531

6.  IL17eScan: A Tool for the Identification of Peptides Inducing IL-17 Response.

Authors:  Sudheer Gupta; Parul Mittal; Midhun K Madhu; Vineet K Sharma
Journal:  Front Immunol       Date:  2017-10-31       Impact factor: 7.561

7.  K-Nearest Neighbor and Random Forest-Based Prediction of Putative Tyrosinase Inhibitory Peptides of Abalone Haliotis diversicolor.

Authors:  Sasikarn Kongsompong; Teerasak E-Kobon; Pramote Chumnanpuen
Journal:  Molecules       Date:  2021-06-16       Impact factor: 4.411

8.  Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins.

Authors:  Ashok K Sharma; Sanjiv Kumar; Harish K; Darshan B Dhakan; Vineet K Sharma
Journal:  BMC Genomics       Date:  2016-05-27       Impact factor: 3.969

9.  Prediction of Biofilm Inhibiting Peptides: An In silico Approach.

Authors:  Sudheer Gupta; Ashok K Sharma; Shubham K Jaiswal; Vineet K Sharma
Journal:  Front Microbiol       Date:  2016-06-16       Impact factor: 5.640

10.  A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota.

Authors:  Ashok K Sharma; Shubham K Jaiswal; Nikhil Chaudhary; Vineet K Sharma
Journal:  Sci Rep       Date:  2017-08-29       Impact factor: 4.379

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