[Bio] / FigTutorial / assignment1.html Repository:
ViewVC logotype

Annotation of /FigTutorial/assignment1.html

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (view) (download) (as text)

1 : overbeek 1.1 <h1>Assignment 1: Getting Started</h1>
2 :     <p>
3 :     The goal of this assignment is to acquaint you with exactly how to use
4 :     the SEED to extract basic information relating to a genome. We assume
5 :     that you know how to access a version of the SEED and that you have
6 :     access to someone that can help you get started.
7 :     <p>
8 :     You need to start by being able to locate specific genes. Suppose
9 :     that you have just been reading an article in the Journal of
10 :     Bacteriology and you wish to connect what you have been reading to
11 :     what you see in the SEED. There are at least two common cases:
12 :     <ol>
13 :     <li>you have a gene name or a function from the article, or
14 :     <li>you have a short fragment of sequence from the article.
15 :     </ol>
16 :     <br>
17 :     <b>Problem 1.1: Locate the gene in <i>Brucella melitensis suis</i> that
18 :     was called BR0018 by the authors of the article describing the
19 :     genome.
20 :     <br>
21 :     Problem 1.2: Locate the gene in <i>Brucella melitensis suis</i> that
22 :     encodes a protein containing the following short amino acid sequence:
23 :     "PTEPVWQGEIQGAGLGMAVDVWNDD".
24 :     </b>
25 :     <br>
26 :     Once you have located a gene, you should be able to figure out
27 :     <ul>
28 :     <li>what functions have been assigned to the gene by different people,
29 :     <li>what biochemical subsystem the gene belongs to,
30 :     <li>what genes from other organisms are similar to the given gene, and
31 :     <li>what annotations have been associated with any of those genes.
32 :     </ul>
33 :     <br>
34 :     <b>Problem 1.3: What functional roles have been assigned to the
35 :     gene BR0018 in <i>Brucella melitensis suis</i>?</b>
36 :     <br>
37 :     Note that the FIG assignment differs from some of the others. Please
38 :     describe the differences (i.e., are the assignments incompatible?).
39 :     <br>
40 :     <b>Problem 1.4: What biochemical subsystem includes the gene, assuming the
41 :     FIG assignment is correct? What other functional roles would you
42 :     expect to exist, assuming the function is accurate?</b>
43 :     <br>
44 :     <b>Problem 1.5: Give the three "closest genes" from other organisms
45 :     based on similarity.</b>
46 :     <br>
47 :     To address problem 1.4, you need to somehow get to KEGG. You can do
48 :     this through the SEED, or you can go directly to that system. If KEGG
49 :     has integrated the organism you are interested in, you can see what
50 :     metabolic functions can be directly connected to genes. If the
51 :     organism is in the SEED, but not KEGG, you will need to go through the
52 :     SEED to
53 :     see what functional roles can be connected to genes.
54 :     In any event, you need to locate the portion of the metabolic reaction
55 :     network that is relevant and try to understand what possible pathways
56 :     the gene might participate in.
57 :     <br>
58 :     Problem 1.5 has a slight wrinkle; you need to understand how the FIG
59 :     similarities are presented and what it means to "expand raw sims".
60 :     Alternatively, you could just use psi-blast to locate the related
61 :     genes/organisms.
62 :     <br>
63 : overbeek 1.2 <b>Problem 1.6:</b> Pick a gene in <i>Staphylococcus aureus subsp. aureus
64 : overbeek 1.1 MW2</i> (say, "recN"). Then, use <b>To Compare Regions</b> to find at
65 :     least 3 genes (from any of the <i>Staph aqureus</i> genomes) that were
66 :     probably miscalled (either not called at all, or had incorrect start
67 :     positions). You need not do the analysis required to determine
68 :     exactly what the correct call should be (which is not something the
69 :     SEED supports very well); just identify where the potential problems
70 :     exist.
71 :     <br>
72 :     To do problem 1.6, you need to first position yourself on a gene from
73 :     the desired genome. This you should know how to do, so do it. Then,
74 :     look down the page. There is a section in which you have links to do
75 :     things like get the DNA sequence, the protein sequence and so forth.
76 :     One of those links should be <b>To Compare Regions</b>. That is the
77 :     one you want. Try it and look at the results. Notice that besides
78 :     seeing a colored display (in which genes that have the same color and
79 :     number are similar), you have a button <b>Commentary</b> that you can
80 :     click on to get a commentary of the functions of the genes in a
81 :     different window.

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3