how can I obtain the fasta file sequence for the 8514 plasmid ?

bioinfo-ut / PlasmidSeeker

A k-mer based program for the identification of known plasmids from whole-genome sequencing reads

BSD 3-Clause "New" or "Revised" License

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how can I obtain the fasta file sequence for the 8514 plasmid ? #16

Closed kjestradag closed 5 years ago

martroosaare commented 5 years ago

just download the database (links provided in publication) - it contains both k-mer list files and associated FASTA files.

LeonardosMageiros commented 5 years ago

Hi,

I would like to do exactly the same thing and obtain a fasta file of the plasmids in your db. Going in the link of your publication (https://figshare.com/articles/PlasmidSeeker_database_k_20/5497972/1) I can only find a binary version of your database. Is there an alternative link that I am missing to get the fasta file(s)?

Thank you very much in advance! Leonardos

mihkelvaher commented 5 years ago

Hi,

The file appears to have been gone missing. I've added the multifasta file to http://bioinfo.ut.ee/plasmidseeker/plasmid_db_12jul17.fna.gz

The fasta headers (in plasmid_db_12jul17.fna) and the "names.txt" (which is with the binary files on figshare), contain all of the info needed. Note that the fasta header also contains the NC accession number if further research is needed.

Regards, Mihkel

LeonardosMageiros commented 5 years ago

Thank you very much Mihkel. I have the fasta file now!

I can see that the db is from 2017. Can I ask if you have any plans of an updated version?

Best Leonardos