Lab 2: Biochemical and Gene Techniques - DNA and Protein Sequence Databases
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Questions and Answers

What does the blastp results page illustrate?

  • The alignment of query sequence with other sequences in the database (correct)
  • The process of designing experiments
  • The function of specific proteins
  • The 3D structure of corn alpha-amylase

    • What does the top red bar in the diagrammatic representation of the blastp results page represent?

  • The query sequence (correct)
  • The conserved sequence regions
  • The hit sequences in the database
  • The protein families

    • What is the primary function of primary databases?

  • To provide a consensus sequence from multiple experiments
  • To separate the wheat from the chaff in a sequence search
  • To identify conserved domains within a protein
  • To store experimental results in an accessible format (correct)

    • What do the two scores at the right of the blastp results page indicate?

    <p>The degree of similarity between sequences</p> Signup and view all the answers

    What is the purpose of multiple alignments of protein sequences?

    <p>All of the above</p> Signup and view all the answers

    What is the purpose of Entrez?

    <p>To provide integrated access to a wide range of data domains</p> Signup and view all the answers

    What is the abbreviation for European Molecular Biology Laboratory?

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

    What is the definition of alignment in the context of bioinformatics?

    <p>The process of lining up two or more sequences to achieve maximal levels of identity</p> Signup and view all the answers

    What is a bioinformatics?

    <p>The merger of biotechnology and information technology</p> Signup and view all the answers

    What is the purpose of a sequence search in Entrez?

    <p>All of the above</p> Signup and view all the answers

    What is the URL of the NCBI website?

    <p><a href="http://www.ncbi.nlm.nih.gov">http://www.ncbi.nlm.nih.gov</a></p> Signup and view all the answers

    What is an algorithm in the context of bioinformatics?

    <p>A procedure embodied in a computer program</p> Signup and view all the answers

    What is the purpose of Clustal Omega?

    <p>To align DNA and protein multiple sequences</p> Signup and view all the answers

    What is the purpose of secondary databases?

    <p>To provide a consensus sequence from multiple experiments</p> Signup and view all the answers

    What is the name of the tool used for basic local alignment search?

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

    What is the first step in using Entrez?

    <p>Go to the NCBI website</p> Signup and view all the answers

    What is the purpose of introducing gaps in an alignment?

    <p>To compensate for insertions and deletions in one sequence relative to another</p> Signup and view all the answers

    What is the primary goal of proteomics?

    <p>To analyze protein expression in normal and diseased tissues</p> Signup and view all the answers

    What is the term for a short conserved region in a protein sequence?

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

    What is the term for a discrete portion of a protein that folds independently?

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

    What is the term for the input sequence used to compare with all entries in a database?

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

    What is the term for the alignment of two nucleic acid or protein sequences over their entire length?

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

    What is the main function of the PubMed link on the NCBI Home Page?

    <p>To search for journal articles on the structure and function of alpha-amylases</p> Signup and view all the answers

    Which of the following BLAST programs compares a nucleotide query sequence against a protein sequence database?

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

    What is the purpose of the tbastx program?

    <p>Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database</p> Signup and view all the answers

    Where can you access the BLAST page from?

    <p>From the Popular Resources menu</p> Signup and view all the answers

    What is the main difference between the blastn and blastp programs?

    <p>The type of query sequence used</p> Signup and view all the answers

    Which of the following is NOT a type of BLAST search?

    <p>Entrez BLAST</p> Signup and view all the answers

    What is the purpose of the blastp program?

    <p>Compares a protein query sequence against a protein sequence database</p> Signup and view all the answers

    Why can't the tblastx program be used with the nr database on the BLAST Web page?

    <p>It is computationally intensive</p> Signup and view all the answers

    Study Notes

    DNA and Protein Sequence Online Databases

    • There are two types of sequence databases: primary and secondary databases
    • Primary databases contain experimental results in an accessible format but are not consensus sequences
    • Secondary databases are curated to reflect consensus sequences from multiple experiments and use primary databases as their sources
    • Examples of primary databases: DDBJ (DNA Databank of Japan), EMBL (European Molecular Biology Laboratory), and GenBank
    • Abbreviations: NCBI (National Center for Biotechnology Information), BLAST (Basic Local Alignment Search Tool)
    • Entrez is a data retrieval system developed by NCBI that provides integrated access to a wide range of data domains
    • Search goals:
      • Identify a representative, well-annotated mRNA or protein sequence record
      • Retrieve associated literature
      • Identify conserved domains within the protein
      • Identify similar proteins
      • Find a resolved three-dimensional structure for the protein or identify structures with homologous sequence
    • Steps to start: Go to the NCBI website, select a database (nucleotide or protein), and search for a gene or protein of interest

    BLAST Introduction

    • BLAST (Basic Local Alignment Search Tool) is a sequence comparison algorithm optimized for speed and sensitivity
    • Selecting a BLAST program: nucleotide blast (blastn), protein blast (blastp), blastx, tblastn, and tblastx
    • BLAST programs compare a query sequence against a database or vice versa

    BLAST Results

    • The blastp results page shows around 100 "Hits", or other protein sequences showing at least some similarity to the query sequence
    • The illustration with red bars is a diagrammatic representation of how the query sequence lines up with other sequences in the database along the primary structure of the protein
    • The two scores at the right (Ident and E value) indicate the degree of similarity

    Clustal Omega and Multiple Sequence Alignment

    • Clustal Omega is a DNA and protein multiple sequence alignment tool
    • Multiple alignments of protein sequences are important tools in studying sequences and provide identification of conserved sequence regions

    Glossary

    • Alignment: The process of lining up two or more sequences to achieve maximal levels of identity and conservation
    • Algorithm: A fixed procedure embodied in a computer program
    • Bioinformatics: The merger of biotechnology and information technology with the goal of revealing new insights and principles in biology
    • Conservation: Changes at a specific position of an amino acid or DNA sequence that preserve the physico-chemical properties of the original residue
    • Domain: A discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function
    • Gap: A space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another
    • Global Alignment: The alignment of two nucleic acid or protein sequences over their entire length
    • Identity: The extent to which two nucleotide or amino acid sequences are invariant
    • Local Alignment: The alignment of some portion of two nucleic acid or protein sequences
    • Motif: A short conserved region in a protein sequence
    • Proteomics: The systematic analysis of protein expression in normal and diseased tissues that involves the separation, identification, and characterization of all of the proteins in an organism
    • Query: The input sequence (or other type of search term) with which all of the entries in a database are to be compared

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    Description

    This quiz covers DNA and protein sequence online databases, including primary and secondary databases, and their role in bioinformatics.

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