PSISearch2D runs query-seeded iterative sequence search for remotely related protein detection. It retrieves Pfam and UniProtKB domain annotation for resulting hits and demonstrates combined domain and sequence alignments in novel visualizations. A scoring model called C-value is newly defined to re-order hits with consideration of the combination of sequence and domain alignments. PSISearch2D improves the predictive performance and is able to characterize unknown proteins in remote protein detection. Together with advanced features of auto-iteration mode to handle large-scale data and optional programs for global and local sequence alignments, PSISearch2D enhances remotely related protein search.

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Yang,M., Zhang,W., Yao,G. et al. Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D.Database (2019) Vol. 2019: article ID baz092;