Finding Plasmids
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11.1 years ago
bioinfo ▴ 840

I have uniprot IDs for 500 genes/gene products. I want to find out whether they can be found in plasmids from a plasmid database using the uniprot IDs and want to extract the corresponding plasmid names. I had a plan to do ID mapping in uniprot using my uniprot IDs but there is no option of any plasmid database to map against. Is there any other plasmid database that has any option like that where I can extract the plasmid names using my 500 uniprot IDs or their fasta sequences in a single run?

plasmid • 5.6k views
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11.1 years ago
Asaf 10k

You cab BLAST them against plasmids (write plasmids under Organism), but this is not one run. You can download the NCBI plasmids database, run BLAST locally against it and with a bit of programming get your table This is not straightforward but should work.

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If I do the local blast after downloading the plasmids, i guess it will take a very long time as I have 500+ genes/FASTA sequences. Lets see what others say otherwise I will give a try with simple BLAST.

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The plasmids database is pretty small

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~ 500 queries versus plasmids should not take very long at all, even on "modest" desktop hardware.

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The link for plasmid database has been updated to:

ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Plasmids/

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