How to Use PSI-BLAST Search Online
Try PSI-BLAST Search
Commercially Available Online Web Server
PSI-BLAST Search: Protein Database Search Programs
PSI-BLAST (Position-Specific Iterated BLAST), a tool that, along with Gapped BLAST, represents are a category of protein database search programs. This suite of programs is a crucial tool for searching protein and DNA databases for sequence similarities. By implementing definitional, algorithmic, and statistical refinements, PSI-BLAST substantially decreases execution time while greatly enhancing sensitivity to weak similarities between protein sequences.
How PSI-BLAST Works
PSI-BLAST and Gapped BLAST introduce several core improvements over previous search methods:
Gapped BLAST Speed-Up: The underlying Gapped BLAST program is significantly faster, running at approximately three times the speed of the original BLAST. This is achieved by combining a new criterion for triggering the extension of word hits with an efficient heuristic for generating gapped alignments.
Iterative Search with PSSM: PSI-BLAST introduces a method for automatically computing and using a position-specific scoring matrix (PSSM) in iterative database searches. In each iteration, the program gathers information from sequences found in the previous round to create a more sensitive PSSM, which helps detect increasingly distant homologs that simple pairwise comparisons might miss.
Enhanced Sensitivity: This iterative PSSM method is key to enhancing the tool's sensitivity to weak similarities, making it ideal for discovering evolutionary and functional relationships between distantly related proteins.
What is Tamarind Bio?
Tamarind Bio is a pioneering no-code bioinformatics platform built to democratize access to powerful computational tools for life scientists and researchers. Recognizing that many cutting-edge machine learning models are often difficult to deploy and use, Tamarind provides an intuitive, web-based environment that completely abstracts away the complexities of high-performance computing, software dependencies, and command-line interfaces.
The platform is designed to provide easy access to biologists, chemists, and other researchers who may not have a background in programming or cloud infrastructure but want to run experimental models with their data. Key features include a user-friendly graphical interface for setting up and launching experiments, a robust API for integration into existing research pipelines, and an automated system for managing and scaling computational resources. By handling the technical heavy lifting, Tamarind empowers researchers to concentrate on their scientific questions and accelerate the pace of discovery.
Accelerating Discovery with PSI-BLAST on Tamarind Bio
Using PSI-BLAST on a platform like Tamarind Bio would provide structural biologists and molecular engineers with a rapid and highly powerful tool for functional and evolutionary annotation.
Discovery of Distant Homologs: Researchers can quickly perform iterative searches to detect faint evolutionary signatures, revealing distant protein relationships that would be missed by standard sequence search methods.
High-Throughput Annotation: The substantial decrease in execution time means the platform can handle high-volume sequence searches for entire proteomes or large libraries of designed proteins, accelerating functional annotation.
Accessible Iterative Search: The platform would manage the complex technical details of automatically computing and applying the position-specific scoring matrix (PSSM), allowing users to focus purely on interpreting the biological significance of the results.
How to Use PSI-BLAST on Tamarind Bio
To leverage PSI-BLAST's power, a researcher could follow this streamlined workflow on Tamarind Bio:
Access our Platform: Begin by logging in to the tamarind.bio website.
Select PSI-BLAST Search: From the list of tiles, either search or select PSI-BLAST Search.
Input a Query Sequence: Provide the amino acid sequence of the protein you wish to analyze.
Set Parameters: Define the iteration count for the iterative search.
Run PSI-BLAST: The platform executes the search, automatically generating and refining the PSSM across multiple search rounds.
Acquire Annotated Homologs: The output provides a list of significant homologs, including those with weak sequence similarity, along with statistical data to evaluate their evolutionary relationship.