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Gene. 2014 Jan 10;533(2):538-40. doi: 10.1016/j.gene.2013.10.015. Epub 2013 Oct 19.

AmphoraNet: the webserver implementation of the AMPHORA2 metagenomic workflow suite.

Author information

1
PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary. Electronic address: kerepesi@pitgroup.org.

Abstract

MOTIVATION:

Metagenomics went through an astonishing development in the past few years. Today not only gene sequencing experts, but numerous laboratories of other specializations need to analyze DNA sequences gained from clinical or environmental samples. Phylogenetic analysis of the metagenomic data presents significant challenges for the biologist and the bioinformatician. The program suite AMPHORA and its workflow version are examples of publicly available software that yields reliable phylogenetic results for metagenomic data.

RESULTS:

Here we present AmphoraNet, an easy-to-use webserver that is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample; the webserver is based on the AMPHORA2 workflow. Since a large proportion of molecular biologists uses the BLAST program and its clones on public webservers instead of the locally installed versions, we believe that the occasional user may find it comfortable that, in this version, no time-consuming installation of every component of the AMPHORA2 suite or expertise in Linux environment is required.

AVAILABILITY:

The webserver is freely available at http://amphoranet.pitgroup.org; no registration is required.

KEYWORDS:

Archaea; Bacteria; Metagenomics; Phylotyping

PMID:
24144838
DOI:
10.1016/j.gene.2013.10.015
[Indexed for MEDLINE]

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