A very brief demo of standard biological/bioinformatics research tools

Hopefully helps you appreciate the kinds of resources available thanks to modern sequencing (and other) techniques and the the Human Genome Project. These are three very popular ones (among probably thousands).

UCSC Genome Browser

We'll use the UCSC Genome Browser to view the CCR5 gene discussed in the Thursday lecture and in the Eric Lander HHMI video.

1. Follow this link to the UCSC genome browser.
2. Change the "position or search term" field to CCR5 and press the "submit" button. A list appears!
3. Choose the top link (in the UCSC Genes list).
4. Check out the display. Each horizontal line ("track") reports data on the CCR5 gene. Some tracks show gene data, such as exon and intron locations, from genome databases (e.g., RefSeq). Other tracks give experimental data (Human mRNAs from GenBank), and others show how conserved CCR5 is across species (Mammal Cons).
5. Look around! Zoom and position controls are at the top. You can specify which tracks are visible with the pulldown menus below.
6. Click on the CCR5 link in the RefSeq track for more information on CCR5. Again, look around. Notice the many links to other resources. Check out the microarray expression data, and the protein structures (models, not based on real crystal structures).

BLAST

Suppose we have a sequence, perhaps from an already sequenced genome, or perhaps new data our Prism 3700 sequencer (a classic?:) just gave us. Wouldn't it be nice to know if some other organism has a similar sequence to give us insights into its function (if it's even a gene).

1. Follow this link to BLAST, a tool for searching for sequence databases.
2. Now follow the Mouse link. We will do a search restricted to the mouse genome.
3. Copy and paste this sequence data into the text box:

   >Mystery gene for demo
   atggattatcaagtgtcaagtccaatctatgacatcaattattatacatc
   ggagccctgccaaaaaatcaatgtgaagcaaatcgcagcccgcctcctgc
   ctccgctctactcactggtgttcatctttggttttgtgggcaacatgctg
   gtcatcctcatcctgataaactgcaaaaggctgaagagcatgactgacat
   ctacctgctcaacctggccatctctgacctgtttttccttcttactgtcc
   ccttctgggctcactatgctgccgcccagtgggactttggaaatacaatg
   tgtcaactcttgacagggctctattttataggcttcttctctggaatctt
   cttcatcatcctcctgacaatcgataggtacctggctgtcgtccatgctg
   tgtttgctttaaaagccaggacggtcacctttggggtggtgacaagtgtg
   atcacttgggtggtggctgtgtttgcgtctctcccaggaatcatctttac
   cagatctcaaaaagaaggtcttcattacacctgcagctctcattttccat
   acagtcagtatcaattctggaagaatttccagacattaaagatagtcatc
   ttggggctggtcctgccgctgcttgtcatggtcatctgctactcgggaat
   cctaaaaactctgcttcggtgtcgaaatgagaagaagaggcacagggctg
   tgaggcttatcttcaccatcatgattgtttattttctcttctgggctccc
   tacaacattgtccttctcctgaacaccttccaggaattctttggcctgaa
   taattgcagtagctctaacaggttggaccaagctatgcaggtgacagaga
   ctcttgggatgacgcactgctgcatcaaccccatcatctatgcctttgtc
   ggggagaagttcagaaactacctcttagtcttcttccaaaagcacattgc
   caaacgcttctgcaaatgctgttctattttccagcaagaggctcccgagc
   gagcaagctcagtttacacccgatccactggggagcaggaaatatctgtg
   ggcttgtga
   

4. Click the "Begin search" button. A new page appears. Click "view report".
5. What do you see?

PDB

1. Go to PDB.
2. In the search field at the top, type GFP,
3. Select the first entry (with ID = 2hgd). What do you get?
4. If you have Java installed, click on the "Jmol" link below the protein structure (graphic). The Jmol applet allows you to interact with the protein model (rotate, zoom, identify atoms/bonds, ...)