BLASTP: different alignment scores depending on which sequence is subject/query

Question

[sam.de.vos]

Hi there,

I'm not sure how active this forum is these days, but I'm hoping for some help on blastp results that I cannot wrap my head around. In order to study similarity between protein regions, I generated my own blastp database and blasted the same fasta file against it;

/bin/makeblastdb -in infile.fasta -dbtype prot -out database   ;

/bin/blastp -db database -query infile.fasta ... (settings)

Therefore, I was expecting to find a lot of duplicate outcomes, where query versus subject sequences would give the same outcome as vice versa. However, in some cases, these pairs of alignments give slightly different outcomes, E.g:

Q:Seq1       (length 32)      S:Seq2        (length 97)      77.778 %id
Q:Seq2       (length 97)      S:Seq1        (length 32)      76.471  %id

After further inspection, it seems that the alignments were not extended the same way:

Q1S2:   QHWGQGTLLTVSSGES       FDLWGRGTLVTVSSGES
Q2S1: YFDLWGRGTLVTVSSGES      YFQHWGQGTLLTVSSGES

Is there a logical explanation how these alignments could differ, based on the direction of the comparison? And is there a way to prevent this?

[JC]

I guess the alignment is scoring different when you open a gap in query that in the target

[sam.de.vos]

I don't think so; there is only a single gap penalty to be set, and it is independent of the AA context.