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easy-search splits perfect full-length nucleotide alignments into two contiguous HSPs unlike BLASTN #1116
Description
Hi,
I’m observing a difference between BLASTN and MMseqs2 (easy-search, version 18.8cc5c) when aligning full-length nucleotide alleles against a bacterial genome.
In multiple cases, BLASTN produces a single perfect alignment (100% identity, 100% coverage), while MMseqs2 splits the same alignment into two perfectly contiguous HSPs with 100% identity.
This happens even when both fragments together exactly reconstruct the full-length BLAST alignment.
Example 1
Blastn result
| qaccver | saccver | pident | length | qcovhsp | mismatch | gapopen | qlen | qstart | qend | sstart | send | evalue | bitscore |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| lmo0027_10 | NODE_4_length_460766_cov_107.215521 | 100 | 1905 | 100 | 0 | 0 | 1905 | 1 | 1905 | 151470 | 149566 | 0 | 3518 |
MMseqs2 result
| qaccver | saccver | pident | length | qcovhsp | mismatch | gapopen | qlen | qstart | qend | sstart | send | evalue | bitscore |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| lmo0027_10 | NODE_4_length_460766_cov_107.215521 | 100 | 1470 | 77.2 | 0 | 0 | 1905 | 1470 | 1 | 150001 | 151470 | 0 | 2635 |
| lmo0027_10 | NODE_4_length_460766_cov_107.215521 | 100 | 435 | 22.8 | 0 | 0 | 1905 | 1905 | 1471 | 149566 | 150000 | 3.28E-226 | 781 |
Example 2
Blastn result
| qaccver | saccver | pident | length | qcovhsp | mismatch | gapopen | qlen | qstart | qend | sstart | send | evalue | bitscore |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| lmo0052_8 | NODE_4_length_460766_cov_107.215521 | 100 | 1974 | 100 | 0 | 0 | 1974 | 1 | 1974 | 121630 | 119657 | 0 | 3646 |
MMseqs2 result
| qaccver | saccver | pident | length | qcovhsp | mismatch | gapopen | qlen | qstart | qend | sstart | send | evalue | bitscore |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| lmo0052_8 | NODE_4_length_460766_cov_107.215521 | 100 | 1630 | 82.6 | 0 | 0 | 1974 | 1630 | 1 | 120001 | 121630 | 0 | 2922 |
| lmo0052_8 | NODE_4_length_460766_cov_107.215521 | 100 | 344 | 17.4 | 0 | 0 | 1974 | 1974 | 1631 | 119657 | 120000 | 4.57E-177 | 618 |
In both cases, MMseqs2 splits the alignment exactly at:
- 150000/150001
- 120000/120001
The two fragments are:
- perfectly contiguous in query and target
- 100% identical
- sum exactly equals the BLASTN alignment length
No sequence discontinuity (no Ns, no gaps, no rearrangements)
Command used:
mmseqs easy-search --search-type 3 --cov-mode 2 -c 0.1 --mask 0 --format-mode 0 -s 7 --split-memory-limit 32G --min-seq-id 0.9 -k 13 --spaced-kmer-mode 0 --max-accept 20 --threads 52 --remove-tmp-files --strand 2 --format-output query,target,pident,alnlen,qcov,mismatch,gapopen,qlen,qstart,qend,tstart,tend,evalue,bits,talnAlso tested with --threads 1, --split-mode 1 and --merge-query 1, and without --split-memory-limit, same behavior
Is this expected behavior of MMseqs2 nucleotide chaining/alignment (i.e. lack of HSP merging across adjacent chains), or is there a parameter that controls merging of adjacent alignments into a single HSP similar to BLASTN?
Thank you in advance
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