MBCN

Search human gut metagenomes metadata and profile, and download them of selected entries. Analyze with them or your own dataset.




Quick Search

The user can filter the entries by using the available main filters or search box in the “Quick search” section. After filtering, the user can download metadata and profile of selected entries, or import them to “Analyze” section.



Advanced Search

The “Advanced search” section provides the user with the ability to search with more complex conditions but slowlier. The user can download metadata and profile of selected entries, or import them to “Analyze” section, too.



Analyze

“Analyze” section provides an interactive way of bioinfomatic analysis online with metadata and profile filtered in search page or uploaded by the user. The user can plot with interactive options and download images.


Database Version

Release 1.0 (June 2021) - 27,641 human gut samples with profile (16,450 of 16S, 11,191 of metagenomics)

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Help


1.Home

The MBCN user interface is divided into three main sections so users can choose the section that better fits their needs. The first section, “Quick search”, holds the full content of the databases' current version, as well as the ability to filter the samples through their main characteristics. The “Advanced search” section provides the user with the ability to search with more complex conditions but slowlier. Finally, the “Analyze” section provides an interactive way of bioinfomatic analysis online with metadata and profile filtered in search page or uploaded by the user.


2. How to use “Quick Search”?

“Quick search” is available for users to access the full content of HumanMetagenomeDB, as well as filter the dataset according to the main available features.

Example usage:

  • All metagenomes metadata will be shown in the Quick search section, including the ones without valid coordinates.
  • You can filter the entries by using the available main filters or by typing in the search box that is placed at the top of the table.
  • After filtering, you can download the metadata of your selected entries as a tab-separated values (.txt) file.
  • At the same time, you can preview and download the profile of your selected entries as a tab-separated values (.txt) file, too.
  • You can import the metadata and profile of your selected entries into “Analyze” by clicking “Import to Analyze” buttom.

3. How to use “Advanced search?”

“Advanced search” section providing to the user the ability to search with more complex conditions but slowlier, especillay when uses the condition of “Equals”. It is recommand to use other condition like “Contains” to speedup

Example usage:

  • All metagenomes metadata will be shown in the Quick search section, including the ones without valid coordinates.
  • You can filter the entries by using the Custom Search Builder at the top of the table by “Add contidion”.
  • After filtering, you can download the metadata of your selected entries as a tab-separated values (.txt) file.
  • At the same time, you can preview and download the profile of your selected entries as a tab-separated values (.txt) file, too.
  • You can import the metadata and profile of your selected entries into “Analyze” by clicking “Import to Analyze” button.

4. How to use “Analyze”

“Analyze” section provides an interactive way of bioinfomatic analysis online with metadata and profile filtered in search page or uploaded by the user.

Example usage:

  • Click “Import to Analyze” button in search page after filtering to upload profile and metadata, and then begin to plot.
  • You can upload your own profile in “OTU table” tab and metadata in “Factor metadata” and “Numeric metadata” tab instead.
  • When you upload your own profile, the first column should be taxonomy name with 7 levels split by '.', ',', ';' or '|'. For example, 'k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium_longum'. Otherwise, you must uploaded an OTUtotax file which contains the 7 levels of the taxonomy in 'OTU to tax table' Page like example. The first column of OTUtotax table should match the first column of profile.
  • When you upload your own metadata, the first column of metadata should be sample ids, which must match column names of OTU table. The factor metadata is necessary for all analysis. The numeric metadata is only needed in “Environmental” analysis tab.
  • You can skip all upload steps and begin analysis with example data.
  • Click “Draw” button to plot and “Download” button to download the plot. If “Download” button doesn't work, you can try to right-click the image of plot to save as png file.

5. What does each attribute of the database mean?


6. Taxonomic assignment to the sequenced reads

MAPseq

MAPseqwas used to analyze 16S data and assign taxonomic classification information to the reads. Relative abundances were then calculated at the genus and species levels for each sample, with the totaling abundance values of 100% respectively.

MetaPhlAn3

MetaPhlAn3 was used with default parameters for the taxonomic classification of metagenomic sequencing reads.


7. Other questions?

Please contact with us by email aetherwalker965@gmail.com