Alignment of the Serine Protease family

Published February 4, 2026 | Version v3

Dataset Open

Dataset containing the files for the alignment of the Serine Protease protein family.

serprot_ref.faa: manually curated alignment of 1390 members of the Serine Protease family for the Halabi Sector paper.
serprot.hmm: HMM profile made using hmmbuild from the serprot_ref.faa alignment.
serprot_matches.stk: Stockholm file containing the output of the hmmsearch on the UniProt database using the serprot.hmm profile.
new_aln0.faa: FASTA file with the MSA after conversion from Stockholm using the stk2fasta.pl script.
new_aln.faa: FASTA file with the MSA after running the code of the 00_alignment_cleaning.ipynb notebook.
iter_aln.faa: FASTA file with the MSA after running the code of the 01_compact_alignment.ipynb notebook.
iter_aln_dedup.faa: FASTA file with the MSA without duplicate sequences.
iter_aln_dedup_sp.faa: FASTA file with the MSA without duplicate sequences, that assigns duplicates possibly to SwissProt candidates.

The last file is currently the most reliable choice for an alignment.

MSA file	MSA description	L (number of positions)	M (number of sequences)
`serprot_ref.faa`	Reference alignment of Serine Proteases, manually curated for the Halabi Sector paper.	823	1 390
`new_aln0.faa`	Alignment coming from the `hmmsearch` using the HMM profile made with `serprot_ref.faa`.	823	189 304
`new_aln.faa`	Alignment coming from the `00_alignment_cleaning.ipynb` notebook.	693	101 543
`iter_aln.faa`	Alignment coming from the `01_compact_alignment.ipynb` notebook.	260	101 543
`iter_aln_dedup.faa`	Alignment coming from the deduplication of `iter_aln.faa`.	260	82 021
`iter_aln_dedup_sp.faa`	Alignment coming from the deduplication of `iter_aln.faa` with possibly SwissProt identifiers.	260	82 021

Files

Name	Size
iter_aln.faa md5:532a5a6da7622e309fefcdc1c8fb8fe0	29.8 MB	Download
iter_aln_dedup.faa md5:f00424c1a4745bb7ec4b82da6f0d3d75	24.0 MB	Download
iter_aln_dedup_sp.faa md5:e55ed8aa76e309c868fe32c9856ff6b5	24.8 MB	Download
new_aln.faa md5:1fd30f9981930ab06ee56555f41f0578	73.7 MB	Download
new_aln0.faa md5:0709bbfc19979ccfa9efaf233b5408f2	163.2 MB	Download
serprot.hmm md5:dca6220ddf78fcc08b02ec1c13a9df7f	383.7 kB	Download
serprot_matches.stk md5:3f25e2c326d3a09d7dd567d40ed6fa3a	1.5 GB	Download
serprot_ref.faa md5:3262a16adf1051da7f8193cb898739b2	1.3 MB	Download