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Open Access Software review

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads

Alexander V Tyakht1*, Anna S Popenko1, Maxim S Belenikin13, Ilya A Altukhov12, Alexander V Pavlenko1, Elena S Kostryukova1, Oksana V Selezneva1, Andrei K Larin1, Irina Y Karpova1 and Dmitry G Alexeev12

Author Affiliations

1 Research Institute of Physico-Chemical Medicine of Russian Federal Medico-Biological Agency (RIPCM), Malaya Pirogovskaya 1a, Moscow, 119435, Russia

2 Moscow Institute of Physics and Technology (MIPT), Institutskii per. 9, Dolgoprudny, Moscow Region, 141700, Russia

3 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov st. 32, Moscow, 119991, Russia

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Source Code for Biology and Medicine 2012, 7:13  doi:10.1186/1751-0473-7-13

Published: 7 December 2012

Abstract

MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors’ knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from http://hmpdacc.org webcite). MALINA is made freely available on the web at http://malina.metagenome.ru webcite. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.

Keywords:
Metagenomics; Human gut microbiota; Web-server; Statistical analysis; Visualization