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. 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