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How To Determine If A Given Species Or Taxon Id Corresponds To A Pathogen Or Not?

I have a list of species for which I need to determine if they are known pathogens. What would be the most elegant way to do it?

Edit: I am more interested in Bacteria and Archea with reference to human. Thanks

mapping
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updated by Ram Ram • written by Dhruv Sakalley • Dhruv Sakalley

Bacteria only? Pathogens to human or in general?

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written by Pawel Szczesny Pawel Szczesny

2 answers

See this inspiring post from Rod Page:

GenBank is a potentially rich source of information on host-parasite relationships. Often sequences of parasites will include information on the name of the host (the example I used was sequence AF131710 from the platyhelminth Ligophorus mugilinus, which records the host as the Flathead mullet Mugil cephalus).

FEATURES             Location/Qualifiers
     source          1..374
                     /organism="Ligophorus mugilinus"
                     /mol_type="genomic DNA"
                     /host="Mugil cephalus"
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written by Pierre Lindenbaum Pierre Lindenbaum

In Addition:

Have a look at the "Pathogenic in" column from this ncbi-bacterial-genomes link.

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written by Naga Naga

I was looking for to download all the genome sequences of all human pathogenic bacteria for last few days here. But no success so far. @Naga: When I click on the "link" to check "Pathogenic in" column, I discovered that the link doesn't work any longer. I didn't find the page. Can you guide me?

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updated by Ram Ram • written by bioinfo bioinfo

Seems summary table have been moved to a different folder.

ftp://ftp.ncbi.nih.gov/genomes/GENOME_REPORTS/ But these txt files doesn't have the "pathogen in" column. It is also not listed here in http://www.ncbi.nlm.nih.gov/genome/browse/

As suggested in the linked-post, just do an empty search by selecting 'disease' in the drop down menu in PATRIC

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updated by Ram Ram • written by Naga Naga

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