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What is Basic Local Alignment Search Tool (BLAST)?

BLAST (Basic Local Alignment Search Tool) is a powerful algorithm and program used extensively in bioinformatics. It's a champion at finding regions of similarity within biological sequences, like DNA or protein sequences.

What are the main features of BLAST?

  • Compares Sequences: BLAST takes a query sequence (e.g., a newly discovered DNA fragment) and compares it against a vast database of known sequences.
  • Statistical Significance: It calculates the statistical significance of any matches found. This helps researchers distinguish between random similarities and those with potential biological meaning.
  • Different Algorithms: BLAST offers various algorithms optimized for different types of comparisons (e.g., nucleotide-nucleotide, protein-protein, protein-nucleotide).

Why is BLAST important?

  • BLAST is a fundamental tool for bioinformatics research.
  • It allows researchers to:
    • Identify unknown sequences by comparing them to known ones, aiding in gene or protein function prediction.
    • Study evolutionary relationships between organisms by analyzing sequence similarities.
    • Design primers for further experiments based on identified regions of similarity.

What are applications of BLAST in practice?

  • Gene Discovery: Researchers can use BLAST to compare newly sequenced DNA to known genes, potentially uncovering novel genes or mutations.
  • Drug Discovery: By identifying proteins involved in diseases, BLAST helps researchers search for potential drug targets.
  • Microbiome Analysis: BLAST is crucial for analyzing the vast amount of sequence data generated in microbiome studies to understand the composition and function of microbial communities.

Practical example

  • Imagine a scientist discovers a mysterious virus. They can use BLAST to compare the viral genome sequence against known databases. If a match is found with a high statistical significance, it suggests the newly discovered virus might be related to a previously identified one, aiding in developing diagnostic tests or treatments.

Critical comments

  • BLAST results require careful interpretation. Similar sequences don't necessarily guarantee identical functions.
  • The choice of the appropriate BLAST algorithm and database is crucial for obtaining meaningful results.
  • With ever-increasing sequence data, interpreting BLAST outputs can be computationally intensive and require expertise.

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Study Guide with flashcards and definitions with Genomics at Utrecht University

Flashcards and definitions with Genomics

Online flashcards with Genomics

  • Centromere
  • Chromatides
  • Chromosomes
  • Sex chromosomes
  • Asexual reproduction
  • Sexual reproduction
  • Mitosis
  • Meiosis
  • Genomics
  • Transcriptomics
  • Proteomics
  • Metabolomics
  • Plasmid
  • Polymerase Chain Reaction
  • Next Generation Sequencing
  • Sanger sequencing
  • RNA-sequencing
  • CRISPR-Cas9
  • Forward genetic screens
  • Reverse genetic screens
  • RNA interference
  • Bioinformatics
  • DNA replication
  • DNA mutation
  • Evolution
  • Horizontal gene transfer (HGT)
  • Virus
  • Microsatellites
  • Basic Local Alignment Search Tool (BLAST)
  • Findable, Accessible, Interoperable, and Reusable data (FAIR data)
  • Phylogenetic tree
  • Insertion
  • Deletion
  • For flashcards and definitions, see the supporting content of this study guide
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