Mutually Remote Domain Homolog Multiple Sequence Alignments

There are seven folders within the dataset described below. This dataset is meant to serve as a benchmark dataset where mutually remote homologs (<30% amino acid identity) have been aligned using various methods. The mTM Alignments (Lyu, et al. 2026) are structural alignments that can be used as a ground truth reference for the other alignment methods and for any new method that is developed. The Raw_Fasta files contain the ungapped sequences for each of 23 SCOP (https://www.ebi.ac.uk/pdbe/scop) families represented. 1)SCOP_PDB_Raw_Fasta-Raw ungapped sequences for 23 SCOP families with mutually remote homologs in each family.2)SCOP_PDB_ClustalO_Alignments-Sequences for 23 SCOP families with mutually remote homologs in each family aligned using Clustal Omega with default parameters.3)SCOP_PDB_MAFFT_Alignments-Sequences for 23 SCOP families with mutually remote homologs in each family aligned using MAFFT with a Blosum30 matrix and default parameters.4)SCOP_PDB_mTM_Alignments--Sequences for 23 SCOP families with mutually remote homologs in each family aligned using mTM-align with default parameters.5)SCOP_PDB_StandBLOSUM30_Alignments-Sequences for 23 SCOP families with mutually remote homologs in each family aligned using Needleman-Wunsch with a Blosum30 matrix (Cock et al. 2009). 6)SCOP_PDB_StandBLOSUM45_Alignments-Sequences for 23 SCOP families with mutually remote homologs in each family aligned using Needleman-Wunsch with a Blosum45 matrix (Cock et al. 2009).7)SCOP_PDB_TCoffee_Alignments-Sequences for 23 SCOP families with mutually remote homologs in each family aligned using TCoffee with default parameters. References and Webserver Locations:Clustal Omega:https://www.ebi.ac.uk/jdispatcher/msa/clustalo Cock, P.J.A., Antao, T., Chang, J.T. et al. (2009).Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422–1423. Lyu, et al, mTM-align2: a server for real-time protein structure database search and alignment, Genomics, Proteomics & Bioinformatics, in press, (2026) MAFFT:https://www.ebi.ac.uk/jdispatcher/msa/mafft mTM Align:https://yanglab.qd.sdu.edu.cn/mTM-align/ T-Coffee:https://www.ebi.ac.uk/jdispatcher/msa/tcoffee