Psi-blast

Definition

Psi-BLAST (Position-Specific Iterated BLAST) is a bioinformatics tool that enhances the standard BLAST (Basic Local Alignment Search Tool) by allowing users to detect distant evolutionary relationships between protein sequences. It achieves this by iteratively refining a position-specific scoring matrix (PSSM) based on the input sequence and hits found in each iteration, making it particularly useful for finding homologous sequences that may not have high similarity in their overall structure.

5 Must Know Facts For Your Next Test

1. Psi-BLAST can be run in multiple iterations, where each iteration refines the PSSM based on the previous results to increase sensitivity in detecting homologous sequences.
2. It allows for better detection of conserved motifs in proteins, even when they are not immediately recognizable due to low sequence similarity.
3. The tool is particularly valuable in annotating newly sequenced genomes by identifying potential functional homologs.
4. Psi-BLAST can significantly reduce false positives compared to traditional BLAST searches by incorporating evolutionary information through the iterative process.
5. This method is widely used in genomics and proteomics for applications such as protein function prediction and evolutionary studies.

Review Questions

• How does psi-blast improve upon the traditional BLAST algorithm in finding homologous sequences?
  • Psi-BLAST enhances the traditional BLAST algorithm by employing an iterative approach that refines the search based on previously identified hits. It constructs a Position-Specific Scoring Matrix (PSSM) that captures conserved amino acid patterns across homologous sequences. This allows psi-blast to detect more distant evolutionary relationships, making it effective in identifying homologs that may not share significant overall sequence similarity.
• Discuss the significance of the E-value in psi-blast and how it influences the interpretation of results.
  • In psi-blast, the E-value is crucial as it provides a statistical estimate of how many hits might be expected to occur by chance given the size of the database. A lower E-value indicates a more significant match between sequences, helping researchers differentiate between true homologs and random similarities. As psi-blast iterates and refines the PSSM, it helps lower E-values for relevant sequences, enhancing confidence in identifying meaningful biological relationships.
• Evaluate the implications of using psi-blast for functional annotation of newly sequenced genomes and its impact on our understanding of protein evolution.
  • Using psi-blast for functional annotation of newly sequenced genomes has substantial implications for understanding protein evolution. By identifying homologous sequences across different organisms, researchers can infer potential functions and evolutionary trajectories of proteins. This insight enables a deeper exploration of molecular functions, adaptive changes, and evolutionary pressures that shaped various protein families. Moreover, it contributes to broader evolutionary studies by revealing conserved motifs and patterns indicative of shared ancestry among diverse species.

Related terms

BLAST:

A widely used algorithm for comparing an input sequence against a database of sequences to find regions of similarity.

E-value: The Expectation value, or E-value, is a statistical measure that indicates the number of hits one can “expect” to see by chance when searching a database of a particular size.

PSSM: Position-Specific Scoring Matrix, which is used to score sequences based on the observed frequencies of amino acids at specific positions in a set of aligned sequences.