Alignment of the Serine Protease family

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.

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