Question: Which software can I use to produce an IPR table from shotgun metagenomics data?
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2.8 years ago by
antonioggsousa90 wrote:

Hello!

I have 9 environmental shotgun metagenomics libraries where the data were assemble (with Ray software) and the protein-coding genes sequences predicted with Glimmer by the bioinformaticians from the sequencing company.

Now, I would like to predict the function of the protein-coding genes in fasta format from the 9 metagenomics datasets in order to produce an IPR table, where the IPRs are the abundance of InterPro hits in the 9 datasets. I mean would like to have the IPRs hits as rows and the samples (n=9) as columns, where the numbers represent the abundance of each IPR (a different one in each row) within each sample.

My question is:

Which software can I use to produce an IPR table from shotgun metagenomics data?

I'm aware of InterProScan, but I don't know if this produces the result that I want or if I have to use it to get the IPR hits and, additionally, use another software to edit/format this table.

Thanks in advance, @renh@

sequencing next-gen gene • 648 views
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