DELTABLAST

Delta-BLAST, or Domain Enhanced Lookup Time Accelerated BLAST, is a sequence similarity search method in the BLAST family. It augments standard BLAST by incorporating conserved domain information to improve sensitivity in detecting distant homologs, beyond what basic sequence similarity can reveal.

The method works by first scanning the query sequence against a conserved domain database (CDD) to identify recognizable domains. For each detected domain, Delta-BLAST builds a position-specific scoring matrix (PSSM) based on the domain’s alignments. This domain-informed PSSM is then used in a subsequent BLAST search to identify homologous regions in target sequences, guiding alignments with domain-level context. The resulting matches typically come with domain annotations and domain-based alignments that aid functional interpretation.

Delta-BLAST is implemented in the NCBI BLAST+ software suite and supports searches for protein sequences as well as translated nucleotide queries. It is particularly useful for annotating proteins with distant homology, where standard BLAST may miss relationships due to limited sequence similarity. The approach leverages the curated domain information in databases such as the Conserved Domain Database (CDD) to enhance detection of remote relationships.

Limitations include dependence on the quality and coverage of the conserved domain database and potential increases in computational cost for large-scale searches. Users may also need to adjust parameters to balance sensitivity and specificity according to their data and research goals.

Delta-BLAST has been adopted in protein annotation and comparative genomics workflows as a method to improve detection of remote homologs and gain insights into protein function. See also: BLAST, PSI-BLAST, Conserved Domain Database, protein homology.