Comparison Of Pathways Between Microbial Genomes
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8.4 years ago
fredulz ▴ 50

I am looking for a straight-forward way to compare metabolic pathways (presence and absence enzymes) in several annotated but not yet published bacterial genomes, it should be non-commercial and can be command-line based.

There used to be a tool "Comparative Pathway Analyzer" (http://nar.oxfordjournals.org/content/36/suppl_2/W433.full) but the service does not exist anymore. Alternatively, I found a command line tool http://carmen.cebitec.uni-bielefeld.de/cgi-bin/index.cgi, but it builds on Kegg databases, which are not freely available. I checked multiple R packages http://bioconductor.org/packages/release/BiocViews.html#___Pathways, eg. pathview, but they do not seem to be what I am looking for.

The ideal output would be a map for each pathway (Kegg-like), colored depending on presence or absence in the input genomes, with data from multiple genomes in one map (and colors changing if an enzyme is present in all of the input genomes).

Anyone has experience with this?

comparative genomics kegg mapping r • 5.7k views
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8.4 years ago
bigmawen ▴ 410

It depends on how to you want to present your data. If you just want to show the summary statistics on the presence of enzymes (or genes/proteins) in multiple genomes, you may use pathview directly. In other words, if you want to color the presence of enzymes in N genomes into N+1 (0,1,2.. N) different levels, you may check the discrete data examples like Figure 6 in the package vignette or tutorial, http://bioconductor.org/packages/release/bioc/html/pathview.html.

Similarly, pathview can visualize metagenomic or microbiome data when the data are mapped to KEGG ortholog pathways (gene IDs in the format of Kxxxxx). In fact, pathview can visualize various types of molecular data, either continuous or discrete, as long as the data can be mapped onto pathways.

If you want to show the presence absence of enzymes of N genomes side by side by dividing each enzyme nodes into N pieces, pathview does not provide the function currently.

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8.4 years ago
sarahhunter ▴ 600

Have you tried using the iPath software?

From the website:

interactive Pathways Explorer (iPath) is a web-based tool for the visualization, analysis and customization of the various pathways maps. Current version provides three different global overview maps:

  • Metabolic pathways: constructed using 146 KEGG pathways, and gives an overview of the complete metabolism in biological systems
  • Regulatory pathways: 22 KEGG regulatory pathways
  • Biosynthesis of secondary metabolites: contains 58 KEGG pathways involved in biosynthesis of secondary metabolites

In addition to the KEGG based overview maps, iPath is used for visualization of various species specific, manually created pathway maps. At the moment, only Mycoplasma pneumoniae and a beta version of Mycobacterium tuberculosis maps are publicly available.

iPath provides extensive map customization and data mapping capablities. Colors, width and opacity of any map element can be customized using various types of data (for example KEGG KOs, COGs or enzyme EC numbers). Our help pages provide the full list of supported data types and required formats. All maps in iPath can be easily converted to various bitmap and vector graphical formats for easy inclusion is your documents or further processing.

This software has been used in comparison of bacterial communities from different soil depths, for example.

EDIT: Sorry, I realise that you said it should be command-line based and this is only available via a web interface but if you contact them, you may be able to get a command-line version..?

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8.1 years ago
bigmawen ▴ 410

Pathview now can plot/integrate/compare multiple states/samples or time series in the same graph in as shown in http://pathview.r-forge.r-project.org/#fig-3.

Here is the package: http://bioconductor.org/packages/release/bioc/html/pathview.html

Please check Subsection 7.2 in the vignette for details. You should be able to show multiple genomes in one plot now. Note that pathview now works with 2300 KEGG species and KEGG Orthology.

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