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