Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe

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Uniclust databases of clustered and deeply annotated protein sequences and alignments (2016, methodology): “gz: archive containing three files with Pfam, SCOP, and PDB annotations, each formatted as tab-separated lists with nine columns: (1,2) identifiers for query and target, (3-5, 6-8) domain start and end-position and total sequence length for both UniProt and database sequence, (9) HHblits E-value.”
CASP10 results compared to those of previous CASP experiments (2013, neutral): “It has been shown that including too many sequences in a multiple sequence alignment leads to less accurate alignments,12 but so far there are no published methods of optimizing sequence inclusion.”
RaptorX: exploiting structure information for protein alignment by statistical inference (2011, unknown): “41.”