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Laboratory 1 ncbi, Entrez, and GenBank


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Laboratory 1

NCBI, Entrez, and GenBank

The purpose of this exercise is for you to gain rudimentary experience using sequence databases (i.e., GenBank) through an online portal (i.e., Entrez). In your web browser, go to the NCBI Entrez website (www.ncbi.nlm.nih.gov/sites/gquery). Provide answers to the following questions.



  1. The last known Tasmanian tiger died in the Hobart Zoo in 1936. DNA sequences have been obtained from museum specimens. (In fact, there is an effort to clone this animal using museum material.) You can retrieve tasmanian tiger sequences using the Taxonomy Browser. Search the taxonomy database for Tasmanian Tiger. How many DNA and protein sequences are there? What genes were cloned? You can build a phylogenetic dataset that could be used to analyze the taxonomic position of the Tasmanian Tiger with the Taxonomy Browser. Click on the Metatheria (Marsupial) link in the lineage of the tiger. How many nucleotide sequences are there for Metatheria? Retrieve the entry for Metatheria and get the nucleotide sequences. In Entrez you can refine the query to include only cytochrome b sequences through the Preview/Index tab. How many marsupial cytochrome b sequences are there? You could save these in FASTA format for use in phylogenetic analysis if you wanted. You could browse up the lineage further to get an outgroup sequence. (4 points)

  2. Michael Crichton's fantasy about cloning dinosaurs, Jurassic Park, contains a putative dinosaur DNA sequence. Use nucleotide-nucleotide BLAST against the default nucleotide database, nr, to identify the real source of the following sequence. What is the real source? Select, copy and paste it into the BLAST form window. This is probably the most common use of nucleotide-nucleotide BLAST: sequence identification, establishing whether an exact match for a sequence is already present in the database. (1 point)

  • >DinoDNA from JURASSIC PARK p. 103 nt 1-1200

  • GCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGC

  • GGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCG

  • TGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGC

  • TGCTCACGCTGTACCTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTG

  • CCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAA

  • AGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAG

  • ATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACT

  • CCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCT

  • GGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGG

  • CCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAA

  • CGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCG

  • CACATGGACGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAA

  • CAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAA

  • GCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGG

  • CTTTCTCAATGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTG

  • ACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCA

  • ACACGACTTAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCC

  • GCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGG

  • CCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGG

  • CCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCT

  1. Substantial data are available for two species of filarial nematodes that are human parasites. Use the Taxonomy Browser to examine the number of nucleotide sequences for the superfamily Filaroidea and determine which two species these are. How many nucleotide and protein sequences are there for each of these two species? Display nucleotide records for each of these. What kinds of sequences are most of these? (2 points)

  2. Search for population and phylogenetic studies on bears in Entrez PopSet. Find the study on brown bears and polar bears and display the alignment. What gene or molecular regions were used in this study? Use the tool bar link to display variations in the alignment. Are there fixed differences in the sequences from the brown bear, Ursus arctos, and the polar bear sequences in the alignment? What if the Ursus arctos sequence from the "ABC" islands (Sequence 7) is removed?

Responses to these questions are due via email as an MS Word file before the next lab period. Name your file as follows: LastName_lab1.doc.





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