Entering edit mode
3 days ago
samuel.himes
•
0
I am using blastx to blast nucleotide sequences against a custom protein database.
Here is a snippet of my output. These are all the HSPs for seq1
against subject1
qseqid | sseqid | qlen | qstart | qend | sstart | send | qcovs | qcovhsp | pident |
---|---|---|---|---|---|---|---|---|---|
seq1 | subject1 | 141 | 139 | 2 | 979 | 1024 | 98 | 33 | 86 |
seq1 | subject1 | 141 | 48 | 74 | 44 | 52 | 98 | 6 | 55 |
seq1 | subject1 | 141 | 95 | 112 | 650 | 655 | 98 | 4 | 50 |
I'm confused by the value of qcovhsp
. Consider the first row. qlen
= 141, qstart
=139, and qend
=2. I would think that the qcovhsp
would be around 97%
(139 - 2) / 141 = .971
Why then is qcovhsp
33? In fact, scrolling through my results I don't see any qcovhsp
values > 33. Does qcovhsp
behave differently in blastx than it does in blastn?
FYI this was the command I used to run blast.
blastx -task blastx \
-db my_protein_db \
-query my_fasta.fasta \
-query_gencode 11 \
-outfmt "6 qseqid sseqid qlen qstart qend sstart send pident qcovhsp qcovs qseq" \
> output.txt