OpenLB
Open Library of Bioscience
Advanced Search
Frontiers in genetics
2019;10 469.

ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data.

Theodoros Koutsandreas, Efthymios Ladoukakis, Eleftherios Pilalis, Dimitra Zarafeta, Fragiskos N Kolisis, Georgios Skretas, Aristotelis A Chatziioannou
Author Information
  1. Theodoros Koutsandreas: Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
  2. Efthymios Ladoukakis: Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
  3. Eleftherios Pilalis: Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
  4. Dimitra Zarafeta: Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
  5. Fragiskos N Kolisis: Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
  6. Georgios Skretas: Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
  7. Aristotelis A Chatziioannou: Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
PMID: 31178894 DOI: 10.3389/fgene.2019.00469

Abstract

Metagenomic analysis of environmental samples provides deep insight into the enzymatic mixture of the corresponding niches, capable of revealing peptide sequences with novel functional properties exploiting the high performance of next-generation sequencing (NGS) technologies. At the same time due to their ever increasing complexity, there is a compelling need for ever larger computational configurations to ensure proper bioinformatic analysis, and fine annotation. With the aiming to address the challenges of such an endeavor, we have developed a novel web-based application named ANASTASIA (automated nucleotide aminoacid sequences translational plAtform for systemic interpretation and analysis). ANASTASIA provides a rich environment of bioinformatic tools, either publicly available or novel, proprietary algorithms, integrated within numerous automated algorithmic workflows, and which enables versatile data processing tasks for (meta)genomic sequence datasets. ANASTASIA was initially developed in the framework of the European FP7 project HotZyme, whose aim was to perform exhaustive analysis of metagenomes derived from thermal springs around the globe and to discover new enzymes of industrial interest. ANASTASIA has evolved to become a stable and extensible environment for diversified, metagenomic, functional analyses for a range of applications overarching industrial biotechnology to biomedicine, within the frames of the ELIXIR-GR project. As a showcase, we report the successful mining of a novel thermostable esterase termed "EstDZ4" from a metagenomic sample collected from a hot spring located in Krisuvik, Iceland.

Keywords

automated pipelines bioinformatics metagenomics next generation sequencing novel enzymes systemic biology

References

Nucleic Acids Res. 2000 Jan 1;28(1):33-6 [PMID: 10592175]
Nat Genet. 2000 May;25(1):25-9 [PMID: 10802651]
Trends Genet. 2000 Jun;16(6):276-7 [PMID: 10827456]
Genome Biol. 2000;1(5):REVIEWS0005 [PMID: 11178260]
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D115-9 [PMID: 14681372]
OMICS. 2005 Spring;9(1):91-105 [PMID: 15805780]
Nucleic Acids Res. 2005 Oct 07;33(17):5691-702 [PMID: 16214803]
Bioinformatics. 2006 Jul 1;22(13):1658-9 [PMID: 16731699]
Nucleic Acids Res. 2006;34(19):5623-30 [PMID: 17028096]
Genome Res. 2007 Mar;17(3):377-86 [PMID: 17255551]
Genome Res. 2008 May;18(5):821-9 [PMID: 18349386]
DNA Res. 2008 Dec;15(6):387-96 [PMID: 18940874]
Microbiol Mol Biol Rev. 2008 Dec;72(4):557-78, Table of Contents [PMID: 19052320]
BMC Bioinformatics. 2009 Oct 28;10:359 [PMID: 19863816]
Nucleic Acids Res. 2010 Jul;38(12):e132 [PMID: 20403810]
Genome Biol. 2010;11(5):207 [PMID: 20441614]
Genome Biol. 2010;11(8):R86 [PMID: 20738864]
Nucleic Acids Res. 2010 Nov;38(20):e191 [PMID: 20805240]
Front Neurosci. 2011 Jan 26;5:8 [PMID: 21293737]
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37 [PMID: 21593126]
IEEE Trans Biomed Eng. 2011 Dec;58(12):3522-7 [PMID: 21846603]
Genome Res. 2011 Dec;21(12):2224-41 [PMID: 21926179]
Curr Opin Biotechnol. 2012 Feb;23(1):9-15 [PMID: 22154470]
Brief Funct Genomics. 2012 Jan;11(1):25-37 [PMID: 22184334]
J Mol Biol. 1990 Oct 5;215(3):403-10 [PMID: 2231712]
Brief Bioinform. 2012 Nov;13(6):646-55 [PMID: 22851513]
Bioinformatics. 2012 Oct 15;28(20):2687-8 [PMID: 22923291]
Genome Biol. 2013 Jan 15;14(1):R2 [PMID: 23320958]
Methods. 2013 Sep 1;63(1):41-9 [PMID: 23816787]
Gigascience. 2013 Jul 22;2(1):10 [PMID: 23870653]
Bioinformatics. 2014 Jul 15;30(14):2068-9 [PMID: 24642063]
Front Cell Dev Biol. 2014 Nov 19;2:70 [PMID: 25478562]
Bioinformatics. 2015 May 15;31(10):1674-6 [PMID: 25609793]
Microb Ecol. 2015 Aug;70(2):411-24 [PMID: 25712554]
PLoS One. 2016 Jan 07;11(1):e0146454 [PMID: 26741138]
BMC Bioinformatics. 2016 Feb 02;17:56 [PMID: 26830926]
FEMS Microbiol Lett. 2016 Apr;363(7):null [PMID: 26936607]
Bioinformatics. 2016 Aug 15;32(16):2520-3 [PMID: 27153620]
J Clin Microbiol. 2016 Aug;54(8):1956-63 [PMID: 27194687]
Comput Struct Biotechnol J. 2016 Aug 26;14:333-40 [PMID: 27642503]
Plant J. 2017 Feb;89(4):789-804 [PMID: 27862469]
Nucleic Acids Res. 2017 Jan 4;45(D1):D353-D361 [PMID: 27899662]
Nucleic Acids Res. 2017 Jan 4;45(D1):D200-D203 [PMID: 27899674]
Sci Rep. 2016 Dec 19;6:38886 [PMID: 27991516]
PLoS One. 2017 Jan 18;12(1):e0169662 [PMID: 28099457]
Genome Res. 2017 May;27(5):824-834 [PMID: 28298430]
BMC Genomics. 2017 Jul 10;18(1):521 [PMID: 28693474]
Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655 [PMID: 29145629]
Gigascience. 2018 Jun 1;7(6): [PMID: 29790941]
Sci Rep. 2018 Aug 13;8(1):12034 [PMID: 30104688]
Biotechnol Adv. 2018 Dec;36(8):2077-2100 [PMID: 30266344]
Gene. 1994 Dec 30;151(1-2):131-5 [PMID: 7828861]
Proteins. 1997 Jul;28(3):405-20 [PMID: 9223186]
Anal Biochem. 1976 May 7;72:248-54 [PMID: 942051]
Genome Res. 1998 Mar;8(3):175-85 [PMID: 9521921]
Journal Article

Word Cloud

Similar Articles

Cited By