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CCB-SB / plsdb

PLSDB pipeline to collect bacterial plasmids from NCBI
https://ccb-microbe.cs.uni-saarland.de/plsdb/
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Download Fasta sequences #7

Closed ayabrown closed 3 years ago

ayabrown commented 3 years ago

Hi, Thanks for this wonderful collection of plasmids DNA. I would like to use the collection as a bowtie index and not a blast db, its there a way to download just the Fasta seqs of the plasmids?

Thanks in advance.

Aya

VGalata commented 3 years ago

Dear @ayabrown,

You can extract the FASTA sequences from the BLAST database which is included in the download.

Assuming that you have downloaded and decompressed the PLSDB archive, and BLAST is installed:

# extract seqs from blastdb
blastdbcmd -entry all -db "plsdb.fna" -out "plsdb.fasta"

Let me know if you have more questions.

Best, Valentina

ayabrown commented 3 years ago

Worked beautifully, Thanks!