Closed chahatupreti closed 3 years ago
Dear @chahatupreti,
Unfortunately, this functionality is currently not implemented in our web server. We might consider to do that in the future. In the meantime, I would download the PLSDB data, filter the accessions by their taxon and use the list of retrieved IDs to filter the FASTA file.
Thanks a lot Valentina. I guess then I will do it the way you suggested. I have 2 follow-up questions if you don't mind -
I used the tsv file, and by filtering by my taxonID of interest, I now have a list of accessions. Now how do I get the FASTA sequences corresponding to these accessions? I tried to open the .fna.nsq file, but it is not normally readable.
The latest data download is PLSDB_2020_06_29, so can I assume that it would probably have all complete plasmids of my organism of interest (E. faecalis) up to June 29?
Thank you so much! Chahat
Dear Chahat,
blast
to extract the sequences from the blast
database files. And I would suggest to use seqkit
to filter that FASTA. See the code below.# extract the files
unzip plasmids__2020_06_29__v0.4.1-6-g8ad6422194.zip
# extract seqs from blastdb
blastdbcmd -entry all -db "plsdb.fna" -out "plsdb.fasta"
# get seq accessions for e. faecalis (tax id 1351)
# column 26 contains the species id, column 2 contains the accessions
awk -F"\t" '$26 == 1351 {print $2}' plsdb.tsv > efaecalis.txt
# filter seqs by their id/accession
seqkit grep -f efaecalis.txt plsdb.fasta -o efaecalis.fasta
I get here 96 records.
If you use conda
, this is how I installed the required tools:
conda create -n test
conda activate test
conda install -c conda-forge -c bioconda blast=2.6.0 seqkit=0.14.0
Let me know if you have further questions!
Best, Valentina
That did it Valentina! Thank you so much for your prompt and very helpful response!!!
Hello!!
Thank you for this excellent resource. I was wondering if it was possible to fetch the plasmid sequences of the species of my interest using PLSDB. I am interested in E.faecalis, and would like to do a search on the plasmids found only in this species. Is this possible?
Thanks in advance!