Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

doi:10.1007/s12275-021-1154-0

. 2021 May;59(5):476-480.

doi: 10.1007/s12275-021-1154-0. Epub 2021 Apr 28.

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

Dongwook Kim ^#¹, Sein Park ^#¹, Jongsik Chun ²

Affiliations

¹ Interdisciplinary Program in Bioinformatics, Institute of Molecular Biology & Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
² Interdisciplinary Program in Bioinformatics, Institute of Molecular Biology & Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea. jchun@snu.ac.kr.

^# Contributed equally.

PMID: 33907973
DOI: 10.1007/s12275-021-1154-0

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

Dongwook Kim et al. J Microbiol. 2021 May.

. 2021 May;59(5):476-480.

doi: 10.1007/s12275-021-1154-0. Epub 2021 Apr 28.

Authors

Dongwook Kim ^#¹, Sein Park ^#¹, Jongsik Chun ²

Affiliations

¹ Interdisciplinary Program in Bioinformatics, Institute of Molecular Biology & Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
² Interdisciplinary Program in Bioinformatics, Institute of Molecular Biology & Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea. jchun@snu.ac.kr.

^# Contributed equally.

PMID: 33907973
DOI: 10.1007/s12275-021-1154-0

Erratum in

Erratum to: Introducing EzAAI: A Pipeline for High Throughput Calculations of Prokaryotic Average Amino Acid Identity.
Kim D, Park S, Chun J. Kim D, et al. J Microbiol. 2023 Sep;61(9):879. doi: 10.1007/s12275-023-00075-z. J Microbiol. 2023. PMID: 37707763 No abstract available.

Abstract

The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and multiple studies have proposed its application in prokaryotic taxonomy and related disciplines. AAI demonstrates better resolution in elucidating taxonomic structure beyond the species rank when compared with average nucleotide identity (ANI), which is a standard criterion in species delineation. However, an efficient and easy-to-use computational tool for AAI calculation in large-scale taxonomic studies is not yet available. Here, we introduce a bioinformatic pipeline, named EzAAI, which allows for rapid and accurate AAI calculation in prokaryote sequences. The EzAAI tool is based on the MMSeqs2 program and computes AAI values almost identical to those generated by the standard BLAST algorithm with significant improvements in the speed of these evaluations. Our pipeline also provides a function for hierarchical clustering to create dendrograms, which is an essential part of any taxonomic study. EzAAI is available for download as a standalone JAVA program at http://leb.snu.ac.kr/ezaai .

Keywords: average amino acid identity; comparative genomics; phylogeny; software suite.

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References

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402. - DOI - PubMed - PMC
1. Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D.R., da Costa, M.S., Rooney, A.P., Yi, H., Xu, X.W., De Meyer, S., et al. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 68, 461–466. - DOI - PubMed
1. Chun, J. and Rainey, F.A. 2014. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int. J. Syst. Evol. Microbiol. 64, 316–324. - DOI - PubMed
1. Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., and Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91. - DOI - PubMed
1. Hunter, J.D. 2007. Matplotlib: A 2D graphics environment. Comput. Sci. Eng. 9, 90–95. - DOI

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[1] Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402. - DOI - PubMed - PMC

[2] Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402. - DOI - PubMed - PMC

[3] Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D.R., da Costa, M.S., Rooney, A.P., Yi, H., Xu, X.W., De Meyer, S., et al. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 68, 461–466. - DOI - PubMed

[4] Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D.R., da Costa, M.S., Rooney, A.P., Yi, H., Xu, X.W., De Meyer, S., et al. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 68, 461–466. - DOI - PubMed

[5] Chun, J. and Rainey, F.A. 2014. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int. J. Syst. Evol. Microbiol. 64, 316–324. - DOI - PubMed

[6] Chun, J. and Rainey, F.A. 2014. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int. J. Syst. Evol. Microbiol. 64, 316–324. - DOI - PubMed

[7] Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., and Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91. - DOI - PubMed

[8] Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., and Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91. - DOI - PubMed

[9] Hunter, J.D. 2007. Matplotlib: A 2D graphics environment. Comput. Sci. Eng. 9, 90–95. - DOI

[10] Hunter, J.D. 2007. Matplotlib: A 2D graphics environment. Comput. Sci. Eng. 9, 90–95. - DOI

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Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

Affiliations

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

Authors

Affiliations

Erratum in

Abstract

References

MeSH terms

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LinkOut - more resources

Full Text Sources

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Molecular Biology Databases

Research Materials