MG-RAST

[…] tx analysis was conducted (). The taxonomic structure of the archaeal community was aligned and annotated with the RefSeq database as a reference (). The taxonomic structure was then exported via the MG-RAST API server () and further visualized using krona tool version 2.7 (). […]

[…] ool samples sequenced over the V1–V3 region of bacterial 16S rDNA were selected for analysis (175 individual human stool samples). Bacterial 16S sequences from the Mongolian humans were obtained from MG-RAST (project no. 8437), while bacterial 16S sequences from the Old World monkeys were obtained from personal correspondence with Suleyman Yildirim (red-tailed guenons, black-and-white colobi, and […]

[…] ntigs). Firstly, de novo assemblies of raw reads were performed using the RAY Meta (Boisvert et al., ) assembler. Secondly, to explore contig features and gene contents, contigs were submitted to the MG-RAST webserver (Glass et al., ) and ORF prediction was conducted using the FragGeneScan tool (Rho et al., ). Afterwards, contigs were annotated with the BLAT tool implemented in MG-RAST against the […]

[…] Currently, several applications are available to users adressing the task of computational metagenome analysis, most notably MG-RAST, IMG/M, and the EBI metagenomics portal. Also, web-based infrastructures such as CyVerse provide some basic capabilities to process metagenome data, and virtual machines like CloVR enable meta […]

[…] f healthy individuals in North and South America []. DNA was sequenced using massively parallel sequencing (454 sequencing) with an average of 1.6·105 reads per sample. The reads were downloaded from MG-RAST database [], and translated into all six reading frames, which were in turn mapped to eggNOG database v4.5 [] using HMMER []. Mapped reads with e-value of max 10−5 were kept. The Marine datase […]

[…] sually involves a best-hit strategy to assign reads to functional classes.Software or websites for analyzing microbiome shotgun sequencing samples usually provide some level of interactivity, such as MG-RAST []. The interactive microbiome analysis tool MEGAN, which was first used in 2006 [], is explicitly designed to enable users to interactively explore large numbers of microbiome samples contain […]