Bioinformatics: Databases and File Formats

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Questions and Answers

Which of the following is NOT a primary application area of bioinformatics?

  • Phylogenetic analysis
  • Quantum entanglement (correct)
  • Sequence alignment
  • Motif discovery

Bioinformatics is best described as an interdisciplinary field because it integrates principles and techniques from which of the following sets of disciplines?

  • Biology, computer science, and information technology (correct)
  • Biology, chemistry and physics
  • Mathematics, statistics, and economics
  • Physics, engineering, and mathematics

Which of the following statements best captures the core aim of bioinformatics?

  • To analyze and interpret biological data through computational methods (correct)
  • To design faster computers for biological research
  • To create graphical representations of biological structures
  • To develop new drugs using chemical principles

Suppose you are searching for genetic information on a specific disease. Which NCBI resource would be most suitable to begin your search?

<p>OMIM (C)</p> Signup and view all the answers

Which NCBI resource is most geared towards providing access to full-text books and reports related to biomedical topics?

<p>Bookshelf (D)</p> Signup and view all the answers

If you have a DNA sequence for a newly discovered gene, which file format would be most suitable for submitting it to a database like GenBank?

<p>FASTA Format (B)</p> Signup and view all the answers

Which file format is commonly used to store aligned sequencing reads and their associated quality scores, especially from next-generation sequencing experiments?

<p>SRA Format (.sra) (D)</p> Signup and view all the answers

You have genomic coordinates indicating the start and end positions of several genes along a chromosome. Which file format would be most appropriate for storing this data?

<p>BED Format (.bed) (A)</p> Signup and view all the answers

Which file format is primarily used for storing hierarchical data, often employed for representing complex biological information with nested elements?

<p>XML Format (A)</p> Signup and view all the answers

Suppose you want to annotate various features (e.g., exons, introns, regulatory regions) on a genome. Which file format would be most suitable for storing these annotations?

<p>GFF (General Feature Format) (D)</p> Signup and view all the answers

Flashcards

Bioinformatics applications

Sequence alignment and motif discovery.

Why is bioinformatics interdisciplinary?

It integrates principles and techniques from multiple scientific disciplines to analyze and interpret biological data, involving biology, computer science, statistics, mathematics and information technology.

Literature links at NCBI

PubMed, PubMed Central (PMC), Bookshelf, Nucleotide database, Protein Database, Gene database, UniGene, OMIM, Entrez Literature.

File formats for data retrieval in NCBI

FASTA, GenBank, FASTQ, GFF (General Feature Format), XML, ASN.1, SRA (.sra), BED (.bed).

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Study Notes

  • Bioinformatics values are expected in areas such as sequence alignment and motif discovery.
  • Bioinformatics is an interdisciplinary field because it integrates principles and techniques from multiple scientific disciplines to analyze and interpret biological data.
  • Bioinformatics involves the intersection of biology, computer science, statistics, mathematics, and information technology.
  • PubMed
  • PubMed Central (PMC)
  • Bookshelf
  • Nucleotide database
  • Protein database
  • Gene database
  • UniGene
  • OMIM
  • Entrez literature

File Formats Available for Data Retrieval

  • FASTA format
  • GenBank format
  • FASTQ format
  • GFF (General Feature Format)
  • XML format
  • ASN.1 format
  • SRA format (.sra)
  • BED format (.bed)

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