Bioinformatics - BLAST Tool Types and Algorithm
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Questions and Answers

What does BLAST stand for?

  • Biochemical Local Alignment Search Tool
  • Basic Local Alignment Search Tool (correct)
  • Biological Local Analysis Search Tool
  • Biological Local Alignment Search Tool

    • TBlastn compares nucleotide query sequences against protein databases.

    False

    What is the function of the E-value in a BLAST search?

    To indicate the statistical significance of a given pairwise alignment.

    BLASTp is used to compare a protein query against a __________ sequence database.

    <p>protein</p> Signup and view all the answers

    Which type of BLAST compares six-frame translation products of a nucleotide query against a protein database?

    <p>Blastx</p> Signup and view all the answers

    Match the following types of BLAST to their corresponding descriptions:

    <p>Blastp = Compares protein query against protein database Blastn = Compares nucleotide query against nucleotide database tBlastn = Compares protein query against translated nucleotide database Blastx = Compares translated nucleotide against protein database</p> Signup and view all the answers

    The word size in a BLAST search indicates the length of the seed that initiates an alignment.

    <p>True</p> Signup and view all the answers

    TBlastx translates both nucleotide query sequences and compares them at the __________ level.

    <p>amino acid</p> Signup and view all the answers

    What is the primary purpose of sequence alignment?

    <p>To infer roles and functions of newly isolated sequences</p> Signup and view all the answers

    Homologous sequences must belong to different species.

    <p>False</p> Signup and view all the answers

    What is the difference between orthologs and paralogs?

    <p>Orthologs are genes in different species that evolved from a common ancestor, while paralogs are genes within the same species that have evolved from gene duplication.</p> Signup and view all the answers

    _____ are genes in different species that evolved from a common ancestral gene through a speciation event.

    <p>Orthologs</p> Signup and view all the answers

    Match the types of alignments with their definitions:

    <p>Global Alignment = Aligns every residue in all sequences from beginning to end. Local Alignment = Aligns regions of sequences that show the highest similarity. Pairwise Alignment = Compares two sequences and identifies the best match. Multiple Sequence Alignment = Compares three or more sequences to identify conserved regions.</p> Signup and view all the answers

    What is the purpose of creating an alignment in sequence analysis?

    <p>To create positional homology</p> Signup and view all the answers

    Adding gaps to sequences can improve the quality of alignment.

    <p>True</p> Signup and view all the answers

    What is Clustal W used for in sequence analysis?

    <p>Creating alignments</p> Signup and view all the answers

    The __________ of the analysis heavily relies on the quality of the alignment.

    <p>quality</p> Signup and view all the answers

    Which step is NOT part of the alignment process?

    <p>Generating random genetic codes</p> Signup and view all the answers

    Match the type of alignment with its description:

    <p>Global Alignment = Aligns entire sequence Local Alignment = Aligns sub-regions of sequences Pairwise Alignment = Compares two sequences Multiple Sequence Alignment = Aligns three or more sequences</p> Signup and view all the answers

    What is the significance of positional homology in alignments?

    <p>It allows for comparison of equivalent positions among sequences.</p> Signup and view all the answers

    BLAST is used for aligning sequences.

    <p>False</p> Signup and view all the answers

    What is the main goal of pairwise alignment?

    <p>To achieve the highest possible score indicating similarity</p> Signup and view all the answers

    Cystic fibrosis is linked to a missing __________ base DNA sequence.

    <p>three</p> Signup and view all the answers

    What is a common application of sequence alignments?

    <p>Analyzing gene variance in populations</p> Signup and view all the answers

    Global alignment compares the entire length of two sequences regardless of their sizes.

    <p>False</p> Signup and view all the answers

    Name one commonly used sequence alignment algorithm.

    <p>Global alignment or Local alignment</p> Signup and view all the answers

    Multiple sequence alignment involves aligning __________ biological sequences to achieve optimal matching.

    <p>three or more</p> Signup and view all the answers

    Match the type of alignment with its description:

    <p>Global alignment = Aligns entire lengths of sequences Local alignment = Aligns regions with highest density of matches Pairwise alignment = Involves two sequences Multiple sequence alignment = Aligns three or more sequences</p> Signup and view all the answers

    What advantage does BLAST offer?

    <p>It provides reliable statistical reports and speed</p> Signup and view all the answers

    Local alignment is used to align the entire length of nucleotide sequences.

    <p>False</p> Signup and view all the answers

    What is the primary use of multiple sequence alignment?

    <p>To identify conserved sequence regions or construct phylogenetic trees</p> Signup and view all the answers

    Homology detection is achieved by analyzing the __________ of sequences.

    <p>similarity</p> Signup and view all the answers

    Which type of alignment is the fundamental operation in bioinformatics?

    <p>Pairwise Alignment</p> Signup and view all the answers

    Study Notes

    BLAST

    • Basic Local Alignment Search Tool
    • Used to compare sequence information
    • Used to retrieve sequences from databases
    • Commonly used in bioinformatics

    BLAST - Types

    • Blastp: Compares protein query against a protein sequence database
    • tBlastn: Compares protein query against translated nucleotide sequence database
    • Blastn: Compares nucleotide query against nucleotide sequence database
    • Blastx: Compares translated nucleotide query against a protein sequence database
    • tBlastx: Compares translated nucleotide query against a translated nucleotide sequence database

    BLAST Algorithm

    • A heuristic program that utilizes shortcuts to speed up searches
    • General parameters:
      • E-Value: Indicates the statistical significance of a given pairwise alignment. Lower E-value signifies greater significance. E-values greater than 1 suggest chance occurrence.
      • Word size: Determines the length of the seed initiating an alignment.
    • Scoring parameters: Reward and penalty for matching and mismatching bases and for creating and extending gaps in an alignment.
    • Filter and masking: Mask regions of low compositional complexity to prevent misleading results.

    BLAST Results

    • The topmost hit represents the best match to the query sequence
    • Flexibility of its search algorithm
    • Reliable statistical reports
    • Continual software development
    • Speed achieved through heuristic search methods

    Sequence Alignment

    • Essential step in comparing biological sequences
    • Identifies regions of similarity between sequences
    • Two types of sequence alignment algorithms:
      • Global alignment: Aligns the entire length of two sequences, best for sequences of equal length.
      • Local alignment: Aligns regions with the highest density of matches, useful for identifying conserved regions.

    Alignment Types

    • Pairwise alignment: Aligns two sequences together, aiming for the highest possible score to indicate similarity.
      • Common applications: Genome analysis, identifying protein relationships, identifying shared domains, basis for BLAST searches.
    • Multiple sequence alignment: Aligns three or more sequences to identify conserved regions.
      • Applications: Identifying conserved regions, constructing phylogenetic trees, understanding evolutionary relationships.

    Why Compare Sequences?

    • Sequence alignments create positional homology, aligning nucleotides at equivalent positions.
    • This allows for the comparison and identification of mutations.
    • A good alignment is crucial for accurate analysis.

    Importance of Sequence Alignments

    • BLAST finds matches.
    • CLUSTAL aligns matches.
    • Alignments facilitate easy comparisons, such as examining how gene sequences vary between people with and without a disease. (e.g., Cystic fibrosis - a missing three-base DNA sequence in affected individuals).

    DNA & Protein Evolution

    • Molecular sequences undergo random changes over time (substitutions, insertions, deletions).
    • Some of these changes are selected for during evolution.

    Homology

    • Indicates that two sequences share a common ancestor recent enough that it is still detectable in their sequence.
    • Requires comparing the same nucleotide sequence in all organisms.

    Orthologs

    • Genes related by vertical descent from a common ancestor.
    • Found in different species and evolved due to speciation events.
    • Typically encode proteins with the same function in different species.

    Paralogs

    • Genes that have evolved within the same species through gene duplication events.
    • Duplicated copies evolve independently, leading to the development of paralogs.
    • Encode proteins with potentially similar, but not identical, functions.

    Orthologs vs. Paralogs

    • Origin: Orthologs - speciation events, Paralogs - gene duplication events.
    • Species: Orthologs - different species, Paralogs - same species.
    • Functionality: Orthologs - retain similar functions, Paralogs - functions can diverge.

    Homology vs. Similarity

    • Homology: Implies a shared common ancestor.
    • Similarity: Can be calculated for any two sequences but is meaningless without homology.

    Alignments: Positional Homology

    • Algorithms, like Clustal W, are used to create alignments.
    • Gaps may be added to sequences to improve alignment quality.
    • Analysis depends on the quality of the alignment.

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    Related Documents

    Lectures 21-22 - BLAST and Sequence Alignment PDF

    Description

    This quiz covers the Basic Local Alignment Search Tool (BLAST) in bioinformatics, focusing on its types such as Blastp, tBlastn, and their functions. Additionally, it explains the BLAST algorithm, including parameters like E-Value and word size. Test your understanding of this essential tool for sequence comparison and retrieval in biological databases.

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