Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server

Methods : a Companion to Methods in Enzymology
Enrico LavezzoStefano Toppo

Abstract

Argot2.5 (Annotation Retrieval of Gene Ontology Terms) is a web server designed to predict protein function. It is an updated version of the previous Argot2 enriched with new features in order to enhance its usability and its overall performance. The algorithmic strategy exploits the grouping of Gene Ontology terms by means of semantic similarity to infer protein function. The tool has been challenged over two independent benchmarks and compared to Argot2, PANNZER, and a baseline method relying on BLAST, proving to obtain a better performance thanks to the contribution of some key interventions in critical steps of the working pipeline. The most effective changes regard: (a) the selection of the input data from sequence similarity searches performed against a clustered version of UniProt databank and a remodeling of the weights given to Pfam hits, (b) the application of taxonomic constraints to filter out annotations that cannot be applied to proteins belonging to the species under investigation. The taxonomic rules are derived from our in-house developed tool, FunTaxIS, that extends those provided by the Gene Ontology consortium. The web server is free for academic users and is available online at http://www.medcomp.medicina.u...Continue Reading

References

Jun 30, 1992·Biochemical and Biophysical Research Communications·S KumarM Noda
Oct 25, 1996·Science·A GoffeauS G Oliver
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Mar 14, 2007·Molecular Systems Biology·Roded SharanRon Shamir
May 9, 2008·BMC Bioinformatics·Catia PesquitaFrancisco M Couto
Aug 6, 2008·BMC Bioinformatics·Meeta Mistry, Paul Pavlidis
Oct 27, 2010·BMC Bioinformatics·Jennifer I Deegan née ClarkChristopher J Mungall
Nov 1, 2011·PLoS Computational Biology·Sean R Eddy
Dec 6, 2011·Briefings in Bioinformatics·Pietro H GuzziMario Cannataro
Jun 14, 2012·PLoS Computational Biology·Nives SkuncaChristophe Dessimoz
Jan 29, 2013·Nature Methods·Predrag RadivojacIddo Friedberg
Nov 30, 2013·Nucleic Acids Research·Robert D FinnMarco Punta
Oct 29, 2014·Nucleic Acids Research·UNKNOWN UniProt Consortium
Nov 16, 2014·Bioinformatics·Baris E SuzekUNKNOWN UniProt Consortium
Jan 13, 2015·International Journal of Proteomics·Arvind Kumar Tiwari, Rajeev Srivastava
Apr 3, 2015·Open Biology·Jessica S Brown, Stephen P Jackson

❮ Previous
Next ❯

Citations

Jan 19, 2016·Methods : a Companion to Methods in Enzymology·Daisuke Kihara
Jan 25, 2017·International Journal of Molecular Sciences·Marta TrevisanLuisa Barzon
May 21, 2019·Nucleic Acids Research·Ronghui YouShanfeng Zhu
Sep 23, 2020·Viruses·Alessandro RossiBas E Dutilh
May 22, 2021·Nucleic Acids Research·Maxat KulmanovRobert Hoehndorf
Sep 26, 2021·Protein Science : a Publication of the Protein Society·Petri Törönen, Liisa Holm

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.