Blastp all sequences agains all sequences, missing comparisons

Question

[Swatchpuppy]

I am running blastp locally with the following commands:

makeblastdb -in sequences.fasta -dbtype prot -out sequences
blastp -db sequences -query sequences.fasta -outfmt 6 -out sequences.tsv -num_threads 4

But not all sequences comparisons figure in the output. Which I was trying to use to cluster the sequences.

Any idea on how to force all comparisons to be made?

Answer 1

[IsmailM]

BLAST is a local alignment tool and is a not a global alignment tool - which is what I suspect you are trying to do based on your question...

BLAST is a good tool if you have a small set of sequences and are looking for potential homologs from a larger dataset.

If you want to align all sequences against all sequence, you need a different alignment program (e.g. mafft).

mafft --maxiterate 1000 --thread 4 sequences.fasta --clustalout > sequences.fasta.out

To install mafft, see this link

Let me know if you need any more help.

On a side note, I would suggest using SequenceServer for running blast (it sets up everything for you and is easier to run).

[Swatchpuppy]

Is there any way for mafft to output the similarity between each sequence pairs? Blast outputs in a table format with that information.