Question: Core proteome using local Blast
gravatar for zarodkip
10 months ago by
zarodkip0 wrote:

Hello all,

I am trying to establish a core proteome of A. baumannii, ie the proteins all of the strains have in common. I have multiple .fasta proteome files.

What would be the most appropriate way of going about this? would this do the trick?:

blastp -query query.fasta -db db -out output.txt -outfmt "6 qseqid qlen sseqid  salltitles pident mismatch gapopen qstart qend qcovs  sstart send evalue bitscore" -evalue 0.00001 -max_target_seqs 5 -num_threads 4

Also, is there a way to run one vs all of my proteomes blast and not one vs one proteome?

I should add I am super new to local blast and using any kind of coding.

local blastp blast core proteome • 255 views
ADD COMMENTlink modified 10 months ago by h.mon32k • written 10 months ago by zarodkip0

What format is your data in? Multi-fasta protein sequence files one per strain? If these are very similar strains (and your dataset is reasonably complete in each case) then you may be able to use CD-HIT to come up with a non-redundant set of proteins which would be equivalent to core proteome.

ADD REPLYlink written 10 months ago by GenoMax96k

Yes, they are multi-fasta sequence files one per strain. I'll look into CD-HIT. Thank you.

ADD REPLYlink written 10 months ago by zarodkip0

I recommend hmmscan (or was it the other hmmsomething) from hmmer against pfam. You get far easier results to interpret this way..

ADD REPLYlink written 10 months ago by 5heikki9.3k
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