Abarenkov, Kessy

Bengtsson, Johan

Eriksson, K. Martin

Grelet, Gwen-Aelle

Hartmann, Martin

Nilsson, R. Henrik

Petri, Anna

Rosenblad, Magnus Alm

Shenoy, Belle Damodara

Wang, Zheng

Antonie van Leeuwenhoek

English

Aberdeen University Research

Bleasby A

DNA technologies: what’s next applied to microbiology research?

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Improved tools for biological sequence comparison.

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Next-generation DNA sequencing.

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Profile hidden Markov models.

Recent developments in the MAFFT multiple sequence alignment program.

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Metaxa : a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics

Eriksson, Martin

Zheng, Wang

Grelet, Gwen-A\ueblle

Alm Rosenblad, Magnus

Chalmers Research

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

https://aura.abdn.ac.uk/bitstream/2164/2562/1/Bengtssonetal2011_open_access.pdf

Metaxa : a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

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