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I am looking to find a way to map a list of biomarkers of interest, say genes or bacterial functions, to existing annotation databases. Usually this is done in reverse, as such that based on metagenomics profiling you can see which pathways or genes are present. However, I want to be able to determine which genes or pathways to extract beforehand i.e. as I think it will be quite difficult to condense pathways or genes of interest from annotation data.

Example:

Biomarker gene for better sleep - maps to annotation database at ... Biomarker gene for glucose metabolism - maps to annotation database at.. .. which in turn allows to directly quantify those biomarkers.

Thanks

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  • $\begingroup$ Hi @alexander and welcome. How do you propose to 'map', are you looking for a specific software tool/website or else custom code? This question is best described as metabolomics.The question needs more clarity. $\endgroup$
    – M__
    Sep 30 '20 at 13:17
  • $\begingroup$ Thanks for your comment. For example, I have a metagenomic dataset with annotated genes, based on this, I want to quantify presence of pathways or related genes of interest. However, finding the relevant genes within the annotated file seems to be labour-intensive. As such, I would want to see which of my genes and pathways of interest are present in the annotated file(s). As such, my question is how to 'find' my genes of interest within the annotated files or used database. $\endgroup$ Sep 30 '20 at 14:48

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