BLASTP

BLASTP is a protein-protein comparison program in the BLAST family that compares a protein query sequence against a protein sequence database to identify homologous sequences.

Using a seed-and-extend approach, BLASTP searches for short exact matches (words) of length three in amino acid sequences, then extends these hits in both directions to form high-scoring segment pairs. It scores alignments with substitution matrices such as BLOSUM62 or PAM, and applies gap penalties to produce gapped alignments.

Results include a list of database hits with statistics such as raw scores, bit scores, and E-values, plus the actual alignments and details about percentage identity and alignment length. Queries and hits are typically submitted in FASTA format, and the database can be a general protein set (non-redundant, NR) or curated collections (Swiss-Prot, UniProt).

BLASTP is commonly used for functional annotation, identification of potential homologs, and inference of conserved domains. It is often used to assess whether a protein shares ancestry with known proteins and to generate hypotheses about function.

Limitations include reduced sensitivity for distant relationships, dependence on database composition, and biases from scoring matrices and gaps. Large databases can be computationally intensive, and interpretations should consider multiple evidence sources.

BLASTP is part of the NCBI BLAST suite and is available via web interfaces and command-line tools. It supports standard outputs and XML or other formats for programmatic use.

Related tools include BLASTN, BLASTX, TBLASTN, TBLASTX, and iterative methods such as PSI-BLAST.