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Phi Blast

The presentation discusses Position-Specific Iterative BLAST (PHI-BLAST), an advanced bioinformatics tool that enhances the traditional BLAST algorithm by utilizing Position-Specific Scoring Matrices (PSSMs) to uncover hidden relationships in biological sequences. PHI-BLAST improves sensitivity in detecting evolutionary connections and aids in identifying novel proteins and predicting their functions. Despite its advantages, effective use of PHI-BLAST requires careful consideration of factors such as query quality and database diversity.

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Sanjida Sampa
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25 views10 pages

Phi Blast

The presentation discusses Position-Specific Iterative BLAST (PHI-BLAST), an advanced bioinformatics tool that enhances the traditional BLAST algorithm by utilizing Position-Specific Scoring Matrices (PSSMs) to uncover hidden relationships in biological sequences. PHI-BLAST improves sensitivity in detecting evolutionary connections and aids in identifying novel proteins and predicting their functions. Despite its advantages, effective use of PHI-BLAST requires careful consideration of factors such as query quality and database diversity.

Uploaded by

Sanjida Sampa
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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PHI-BLAST: Unveiling

Hidden Relationships in
Biological Sequences
This presentation explores the power of Position-Specific
Iterative BLAST (PHI-BLAST) as a valuable tool in
bioinformatics for uncovering hidden relationships and
patterns within biological sequences.
Presented By:

S M Nasimul Hasan
IT-21026
2020-2021

Niloy Sarkar Uthso


IT-21012
2020-2021
Introduction to BLAST and its
Limitations
BLAST (Basic Local Alignment Search Tool) is a However, BLAST's limitations arise when dealing
foundational algorithm for comparing biological with sequences that lack strong overall similarity
sequences like DNA or protein. It identifies regions but share conserved functional motifs or domain
of similarity between a query sequence and a structures. This can lead to missed connections
database of known sequences. and an incomplete understanding of evolutionary
relationships.
What is Position-Specific
Iterative BLAST (PHI-
BLAST)?
PHI-BLAST (Position-Specific Iterative BLAST) is an enhanced
version of BLAST that leverages the concept of Position-
Specific Scoring Matrices (PSSMs) to uncover hidden
relationships between sequences.
The Power of Position-Specific Scoring Matrices
(PSSMs)
PSSMs are statistical models that capture the likelihood of different amino acids occurring at specific
positions within a sequence, especially within conserved functional regions.
How PHI-BLAST Works: An Iterative Search
Process
PHI-BLAST begins by aligning the query sequence The PSSM is used to conduct subsequent
against a database, just like standard BLAST. It iterations of the search, identifying sequences
then uses the alignment results to create a PSSM that match the pattern even with low overall
that represents the conserved pattern. similarity. This iterative process refines the search
and unveils hidden relationships.
Case Study 1: Identifying
Novel Proteins with
Conserved Domains
PHI-BLAST has been successful in identifying novel proteins
that share conserved domains with known proteins, even
when overall sequence similarity is low, expanding our
understanding of protein families and functions.
Case Study 2: Predicting
Protein Function and
Structure
By analyzing the conservation patterns within PSSMs, PHI-
BLAST can provide valuable insights into the function and
structure of proteins, aiding in the prediction of protein
behavior and evolution.
Advantages of PHI-BLAST
over Standard BLAST
PHI-BLAST offers several advantages over standard BLAST,
including increased sensitivity for detecting distant
evolutionary relationships and a greater capacity for finding
sequences with conserved functional motifs.
Challenges and
Considerations for
Effective PHI-BLAST Usage
While PHI-BLAST is a powerful tool, its effectiveness depends
on factors like the quality of the query sequence, the size
and diversity of the database, and the selection of
appropriate parameters.
Conclusion: PHI-BLAST's
Impact on Bioinformatics
Research
PHI-BLAST has revolutionized bioinformatics research by
providing a more sensitive and robust method for identifying
distant relationships between biological sequences,
ultimately contributing to a deeper understanding of the
evolution and function of biological systems.

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