SHOOT: Phylogenetic Gene Search and Ortholog Inference

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2022 Mar 29

PMID 35346327

Authors

David Mark Emms

Steven Kelly

Affiliations

Soon will be listed here.

Abstract

Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees and returns a tree with the query sequence correctly placed within it. We show that SHOOT performs this analysis with comparable speed to a BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional tree inference, and it can identify orthologs with high accuracy. In summary, SHOOT is a fast and accurate tool for phylogenetic analyses of novel query sequences. It is available online at www.shoot.bio .

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References

Altenhoff A, Garrayo-Ventas J, Cosentino S, Emms D, Glover N, Hernandez-Plaza A . The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res. 2020; 48(W1):W538-W545. PMC: 7319555. DOI: 10.1093/nar/gkaa308. View

Mirdita M, Steinegger M, Soding J . MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics. 2019; 35(16):2856-2858. PMC: 6691333. DOI: 10.1093/bioinformatics/bty1057. View

Lipman D, Pearson W . Rapid and sensitive protein similarity searches. Science. 1985; 227(4693):1435-41. DOI: 10.1126/science.2983426. View

Nakamura T, Yamada K, Tomii K, Katoh K . Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics. 2018; 34(14):2490-2492. PMC: 6041967. DOI: 10.1093/bioinformatics/bty121. View

Huerta-Cepas J, Serra F, Bork P . ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol Biol Evol. 2016; 33(6):1635-8. PMC: 4868116. DOI: 10.1093/molbev/msw046. View

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas P . PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2009; 38(Database issue):D204-10. PMC: 2808919. DOI: 10.1093/nar/gkp1019. View

Shank S, Weaver S, Kosakovsky Pond S . phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. BMC Bioinformatics. 2018; 19(1):276. PMC: 6060545. DOI: 10.1186/s12859-018-2283-2. View

Emms D, Kelly S . OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019; 20(1):238. PMC: 6857279. DOI: 10.1186/s13059-019-1832-y. View

Tang H, Finn R, Thomas P . TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Bioinformatics. 2018; 35(3):518-520. PMC: 6361231. DOI: 10.1093/bioinformatics/bty625. View

10.

Hauser M, Steinegger M, Soding J . MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinformatics. 2016; 32(9):1323-30. DOI: 10.1093/bioinformatics/btw006. View

11.

Steinegger M, Soding J . MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017; 35(11):1026-1028. DOI: 10.1038/nbt.3988. View

12.

Cantalapiedra C, Hernandez-Plaza A, Letunic I, Bork P, Huerta-Cepas J . eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol Biol Evol. 2021; 38(12):5825-5829. PMC: 8662613. DOI: 10.1093/molbev/msab293. View

13.

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

14.

Czech L, Barbera P, Stamatakis A . Methods for automatic reference trees and multilevel phylogenetic placement. Bioinformatics. 2018; 35(7):1151-1158. PMC: 6449752. DOI: 10.1093/bioinformatics/bty767. View

15.

Emms D, Kelly S . Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench. Genome Biol Evol. 2020; 12(12):2258-2266. PMC: 7738749. DOI: 10.1093/gbe/evaa211. View

16.

Edgar R . Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26(19):2460-1. DOI: 10.1093/bioinformatics/btq461. View

17.

Huerta-Cepas J, Bueno A, Dopazo J, Gabaldon T . PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res. 2007; 36(Database issue):D491-6. PMC: 2238872. DOI: 10.1093/nar/gkm899. View

18.

Buchfink B, Reuter K, Drost H . Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021; 18(4):366-368. PMC: 8026399. DOI: 10.1038/s41592-021-01101-x. View

19.

Howe K, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode M . Ensembl 2021. Nucleic Acids Res. 2020; 49(D1):D884-D891. PMC: 7778975. DOI: 10.1093/nar/gkaa942. View

20.

NEEDLEMAN S, Wunsch C . A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970; 48(3):443-53. DOI: 10.1016/0022-2836(70)90057-4. View