Psi-blast

Definition

Psi-BLAST (Position-specific Iterated BLAST) is an advanced variation of the original BLAST algorithm used for searching protein and DNA sequences against databases. It enhances the sensitivity of sequence alignment by using position-specific scoring matrices, which consider the frequency of amino acids at each position, allowing for more accurate identification of homologous sequences across evolutionary distances.

5 Must Know Facts For Your Next Test

1. Psi-BLAST iteratively refines the search results by generating a PSSM from initial hits, allowing it to capture more distant homologous sequences.
2. It allows for multiple rounds of searches, where each iteration builds on the previous one to enhance detection sensitivity.
3. The method helps identify conserved domains and motifs across diverse protein families, aiding in functional annotation.
4. Psi-BLAST can reveal evolutionary relationships between sequences, providing insights into protein function and structure.
5. The algorithm is particularly useful in large databases where traditional BLAST may miss relevant hits due to its more stringent matching criteria.

Review Questions

• How does Psi-BLAST improve upon the original BLAST algorithm in terms of sensitivity and accuracy?
  • Psi-BLAST improves on the original BLAST algorithm by employing an iterative approach that uses position-specific scoring matrices. In each iteration, it builds a PSSM from previously identified hits, allowing the algorithm to recognize more distant homologous sequences that might be overlooked by standard BLAST. This enhanced sensitivity leads to more accurate alignments and better identification of evolutionary relationships between sequences.
• What role do Position-specific scoring matrices (PSSMs) play in the functionality of Psi-BLAST?
  • Position-specific scoring matrices (PSSMs) are central to Psi-BLAST's functionality as they provide a refined scoring system based on the frequency of each amino acid at specific positions within aligned sequences. By incorporating these frequencies, Psi-BLAST captures the variability and conservation at each position, enabling it to detect homologous sequences with greater accuracy. This approach allows the algorithm to adapt to different regions within protein families, highlighting conserved domains and aiding in functional predictions.
• Evaluate the impact of using Psi-BLAST on evolutionary studies and functional annotation in molecular biology.
  • Using Psi-BLAST has significantly impacted evolutionary studies and functional annotation by enhancing our ability to detect homologous sequences across diverse organisms. The iterative nature and PSSMs allow researchers to identify conserved domains and motifs that are critical for understanding protein function and evolutionary relationships. This powerful tool not only provides insights into how proteins have evolved but also assists in annotating functions of unknown proteins by linking them to known families, ultimately contributing to our broader understanding of biological processes.

Related terms

BLAST:

Basic Local Alignment Search Tool (BLAST) is a widely used algorithm for comparing an input sequence against a database to find regions of similarity.

E-value: The Expectation value (E-value) is a statistical measure that indicates the number of times one can expect to see a match by chance when searching a database.

PSSM: Position-specific scoring matrix (PSSM) is a matrix used in bioinformatics that describes the likelihood of each amino acid occurring at each position in a sequence alignment.