Real Time Metagenomics: Using k-mers to annotate metagenomes

Robert A. Edwards; Robert Olson; Terry Disz; Gordon D. Pusch; Veronika Vonstein; Rick Stevens; Ross Overbeek

doi:10.1093/bioinformatics/bts599

Real Time Metagenomics: Using k-mers to annotate metagenomes

Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross Overbeek

Research output: Contribution to journal › Article › peer-review

37 Citations (Scopus)

34 Downloads (Pure)

Abstract

Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http://edwards.sdsu.edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed.org/. FIGfams and k-mers are available for download from ftp://ftp.theseed.org/FIGfams/.

Original language	English
Pages (from-to)	3316-3317
Number of pages	2
Journal	Bioinformatics
Volume	28
Issue number	24
DOIs	https://doi.org/10.1093/bioinformatics/bts599
Publication status	Published - Dec 2012
Externally published	Yes

Bibliographical note

© The Author 2012. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Supplementary data

Access to Document

10.1093/bioinformatics/bts599Licence: CC BY

Published versionFinal published version, 110 KBLicence: CC BY

Cite this

@article{cb4751ba592b4bbd9ad83b940b527b3c,

title = "Real Time Metagenomics: Using k-mers to annotate metagenomes",

abstract = "Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http://edwards.sdsu.edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed.org/. FIGfams and k-mers are available for download from ftp://ftp.theseed.org/FIGfams/.",

author = "Edwards, {Robert A.} and Robert Olson and Terry Disz and Pusch, {Gordon D.} and Veronika Vonstein and Rick Stevens and Ross Overbeek",

note = "{\textcopyright} The Author 2012. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Supplementary data",

year = "2012",

month = dec,

doi = "10.1093/bioinformatics/bts599",

language = "English",

volume = "28",

pages = "3316--3317",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "24",

}

TY - JOUR

T1 - Real Time Metagenomics

T2 - Using k-mers to annotate metagenomes

AU - Edwards, Robert A.

AU - Olson, Robert

AU - Disz, Terry

AU - Pusch, Gordon D.

AU - Vonstein, Veronika

AU - Stevens, Rick

AU - Overbeek, Ross

N1 - © The Author 2012. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Supplementary data

PY - 2012/12

Y1 - 2012/12

N2 - Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http://edwards.sdsu.edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed.org/. FIGfams and k-mers are available for download from ftp://ftp.theseed.org/FIGfams/.

AB - Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http://edwards.sdsu.edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed.org/. FIGfams and k-mers are available for download from ftp://ftp.theseed.org/FIGfams/.

UR - http://www.scopus.com/inward/record.url?scp=84870854663&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/bts599

DO - 10.1093/bioinformatics/bts599

M3 - Article

C2 - 23047562

AN - SCOPUS:84870854663

SN - 1367-4803

VL - 28

SP - 3316

EP - 3317

JO - Bioinformatics

JF - Bioinformatics

IS - 24

ER -

Real Time Metagenomics: Using k-mers to annotate metagenomes

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this