jcvi edited this page Sep 14, 2010 · 7 revisions

View Dataset The view pages provide high level summaries of metagenomics datasets. Summaries include top species, KEGG metabolic pathways, Gene Ontology terms, Enzyme Classification IDs, HMMs (such as TIGRFAM and Pfam HMMs) and functional names.

Browse Dataset Metagenomics annotations can be browsed using four distinct hierarchies: NCBI Taxonomy, Gene Ontology, Enzyme Classification and KEGG metabolic pathways.

Search Dataset Users can use a SQL like query syntax including logical combinations of annotation fields to filter datasets. For example a user may filter results based on the BLAST E-Value or combination of BLAST E-Value and percent identity, search for only bacterial species, or choose to exclude results that have BLAST hits to eukaryotes.

Compare Multiple Datasets The compare page allows each user to compare their own datasets, or compare them with datasets shared by other users. The page features a select box to chose datasets. Users can also filter the shown datasets by entering a search keyword. Furthermore, users can specify a query (using the Lucene query language) to filter all selected datasets before the comparison. For example, users may want to only compare hits below a certain similarity search E-Value. A minimum absolute count can be entered bu users to filter out categories with only a few hits. Various comparison options can be selected such as absolute and relative counts, statistical tests multidimensional scaling, heatmap and hierarchical cluster plots. Similar to the View pages, users can choose from several tabs to indicate the annotation data type they wish to compare. Choices are NCBI Taxonomy, Gene Ontology terms, KEGG metabolic pathways, Enzyme Classification, HMMs, and functional descriptions. Absolute and relative counts as well as statistics can be exported in tab delimited format. Graphics can be exported in PDF format.

Heatmap Plot

Hierarchical Clustering Plot


Download Associated Data Besides tab delimited files, users can download sequence and/or annotation data that is linked with a dataset or a collection of datasets using METAREP’s FTP infrastructure.