Question: Finding Plasmids
0
gravatar for bioinfo
6.5 years ago by
bioinfo740
bioinfo740 wrote:

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?

bioinformatics tools database • 3.9k views
ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by bioinfo740
0
gravatar for Asaf
6.5 years ago by
Asaf6.3k
Israel
Asaf6.3k wrote:

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.

ADD COMMENTlink written 6.5 years ago by Asaf6.3k

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.

ADD REPLYlink written 6.5 years ago by bioinfo740

The plasmids database is pretty small

ADD REPLYlink written 6.5 years ago by Asaf6.3k

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

ADD REPLYlink written 6.5 years ago by Neilfws48k

The link for plasmid database has been updated to:

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

ADD REPLYlink written 16 months ago by Prakki Rama2.3k
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