Question: Database annotation for metaproteomics
gravatar for marlenejensen
12 months ago by
marlenejensen20 wrote:

Hey all,

I am using a metaproteomic database for the gut microbiome of mice which I found online

Unfortunately, the accession numbers and protein descriptions are not really helpful for taxonomic analyses since they are like this:

S-Fe7_GL0014216    [gene]  locus=scaffold66956_1:1:1053:+ [Lack both ends] codon-table.11

There is no pattern in the accession in terms of taxonomy and the database is too big for my excel.

The owners also included a text file with explanations of each accessions e.g.

S-Fe7_GL0014216    1/1    Clostridiales    order    root|cellular organisms|Bacteria|Firmicutes|Clostridia|Clostridiales    no rank|no rank|superkingdom|phylum|class|order

I am wondering if there is joint command or script to loop through the file and replace the matching accession with the actual species description?

Thanks in advance for your help!


next-gen • 239 views
ADD COMMENTlink modified 12 months ago by RamRS27k • written 12 months ago by marlenejensen20

the database is too big for my excel

via t@tim_yates

Time to switch to R/Python :-)

ADD REPLYlink modified 12 months ago • written 12 months ago by RamRS27k
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