Homework # 1: Using Databases and Sequence alignment programs

Due January 17, 2003

Please send me your answers by email. You can either create a new file, or download the ms word file and type in your answers.

Part I: Learning about NCBI

1. Go to the National Center for Biotechnology homepage ( http://www.ncbi.nlm.nih.gov ), What does NCBI do?
2. Click on About NCBI (Second heading on the left side of the page), then databases and tools.
   • How many literature databases are at NCBI?
   • What is PROW?
   • How many nucleotide databases are at NCBI?
   • What is UniGene?
   • How many Entrez databases are there?
   • What is Entrez?
   • What is CDD?
   • How many tools are available for 3-D structure display?
   • How many different kinds of maps are available?
3. Return to the NCBI homepage and click on PubMed. What does PubMed do?
4. Return to the NCBI homepage and click on BLAST, then on Blast overview What is BLAST and what does it do?
5. Return to the NCBI homepage and click on OMIM. What is OMIM, and how can you use it?
6. Return to the NCBI homepage and click on Books. How many books are available online at the Bookshelf?
7. Return to the NCBI homepage and click on TaxBrowser. How many organisms are represented at Genbank?
8. Return to the NCBI homepage and click on Structure. What is MMDB?
   
9. I also recommend that you download and install Cn3D on your home computer if that is mainly what you will be using for this course.
   

Part II: Using Entrez:

1. Go to Entrez (http://www.ncbi.nlm.nih.gov/Entrez), select PubMed and type in the word enoyl-ACP reductase. How many hits do you obtain?
2. Now search Protein for enoyl-ACP reductase. How many hits do you obtain?
3. Now search Nucleotide for enoyl-ACP reductase. How many hits do you obtain?
4. Now search Structure for enoyl-ACP reductase. How many hits do you obtain?
5. Click on 1LXC, then on view 3D structure with CN3D. Take a picture of the resulting image, and attach it to your file.

Part III: Interpreting flatfiles

1. Now search Nucleotide for enoyl-ACP reductase and select AY083164.
2. What is the locus of this clone?
3. What is the accession of this clone?
4. What is the common name of the organism?
5. Who are the authors?
6. Where do they work?
7. How long is the clone (in base pairs)?
8. Where does the coding sequence start and finish?
9. How many amino acids does it have?
10. What are the first and the last five amino acids?
11. What is the accession number of the encoded protein?

Part IV: other genomic databases

 
1. Go to the DNA databank of Japan (DDBJ): http://www.ddbj.nig.ac.jp/
2. Find a Database search function that is not available at NCBI.
3. Find a Data analysis function that is not available at NCBI.
4. Find a Protein Database and Structure function that is not available at NCBI.
5. Go to the European Bioinformatics Institute http://www.ebi.ac.uk/
6. Select Bioinformatics Products and Services
7. Find a Database that is not available at NCBI.
8. Find a sequence analysis tool (in the toolbox) that is not available at NCBI.
9. Which of these three sites do you find easiest to navigate?
10. Go to TIGR: http://www.tigr.org/
11. Find a Database that is not available at NCBI.
12. Find a software tool that is not available at NCBI.
    

Part V: other databases

Pick a database from each category on the week 1 websites page. For each, tell me the URL, who maintains it, and what sort of data is stored at it.