Podcast
Questions and Answers
What does the blastp results page illustrate?
What does the top red bar in the diagrammatic representation of the blastp results page represent?
What is the primary function of primary databases?
What do the two scores at the right of the blastp results page indicate?
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What is the purpose of multiple alignments of protein sequences?
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What is the purpose of Entrez?
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What is the abbreviation for European Molecular Biology Laboratory?
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What is the definition of alignment in the context of bioinformatics?
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What is a bioinformatics?
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What is the purpose of a sequence search in Entrez?
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What is the URL of the NCBI website?
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What is an algorithm in the context of bioinformatics?
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What is the purpose of Clustal Omega?
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What is the purpose of secondary databases?
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What is the name of the tool used for basic local alignment search?
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What is the first step in using Entrez?
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What is the purpose of introducing gaps in an alignment?
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What is the primary goal of proteomics?
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What is the term for a short conserved region in a protein sequence?
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What is the term for a discrete portion of a protein that folds independently?
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What is the term for the input sequence used to compare with all entries in a database?
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What is the term for the alignment of two nucleic acid or protein sequences over their entire length?
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What is the main function of the PubMed link on the NCBI Home Page?
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Which of the following BLAST programs compares a nucleotide query sequence against a protein sequence database?
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What is the purpose of the tbastx program?
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Where can you access the BLAST page from?
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What is the main difference between the blastn and blastp programs?
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Which of the following is NOT a type of BLAST search?
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What is the purpose of the blastp program?
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Why can't the tblastx program be used with the nr database on the BLAST Web page?
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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 and Sequence Search
- 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.