Bioinformatics: An Interactive Introduction to NCBI

Created by Seth Bordenstein, Marine Biological Laboratory


Module 1: Sequence Taxonomy

Introduction Module 1 Module 2 Online Resources for Educators

Objective

PCR machines

The goal of this module is to introduce you to the number and diversity of nucleotide sequences in the NCBI database.



Let's Begin!

Begin by linking to the NCBI homepage (www.ncbi.nlm.nih.gov). If you ever get lost, always return to this page as a starting point. Select TaxBrowser at the top right. The NCBI Taxonomy database contains the names of those organisms whose sequences have been deposited. Only a small fraction of the millions of species estimated to exist on earth is represented! Select the option Taxonomy Statistics in the middle of the left-side navigation bar.

  1. For the year 2005, how many new Bacterial species were added to the sequence database?
    2. For the year 1999, how many new Bacterial species were added to the sequence database? Wow, what a difference six years makes!

    Interestingly, the sequence data from extinct organisms are even listed in the GenBank database. Let's look for a gene sequence from a 120 Mya old insect preserved in amber! From your last website,
  • Select the Taxonomy option in the right of the menu bar
  • Select Taxonomy home in the left-hand navigation
  • Select Extinct organisms in the left-hand navigation to see the organism list
  • Scroll down to Insects on the main page and select Libanorhinus succinus(a beetle from Lebanese amber 120-135 Mya).
  • This page gives you very specific information about the ancestry of this organism. Select the option Arthropoda
  • What are some other organisms that belong to this phylum of animals? Can you think of any body traits that these organisms have in common?
  • Go back one page. How many nucleotide sequences have been deposited into the Entrez Records for this organism?
  • What is the name of the gene that was sequenced for this organism? (to find out, click on the number 1 next to nucleotide)
  • How many nucleotide base pairs does this DNA entry contain? (the answer is in the first line of the flatfile after you select the Identification link)


    • Scroll through the complete reference report on this sequence. A lot of information may seem confusing, but it is all there to provide scientists with as much information as possible about this sequence. At the bottom of the screen, you will find the nucleotide sequence (all of the A,T,G,C base pairs) of this gene. Click on the PubMed 8505978 to directly link to the title, authors, and abstract of the published paper! Amazing, now you can read the research article that discovered this nucleotide sequence.

  • Select the NCBI link in the top left corner of the screen (next to the DNA symbol) to return to the NCBI home page. Great! That's where we started with Module 1.

    • Continue to Module 2

    Nasonia vitripennis female using her ovipositor to lay her eggs inside the host fly pupa

    Sequence Searching and BLAST: This module will show you how to retrieve genetic sequence data from the NCBI database that identifies a particular Wolbachia sequence.



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