BCB 444/544 Fall 07 Nov 12 HW6 p1of 1
BCB 444/544
Homework 6 (16 pts)
Due Mon Nov 26 by 5 pm
Name _________________________________________
(Please bring to class or deliver to MBB 106)
Objectives:
1. To provide students with the opportunity to explore functional and comparative genomics resources.
Introduction:
We’ve covered a few aspects of genomic sequencing, comparative genomics and functional genomics in lecture, but
won’t have time to discuss many valuable resources in either lecture or lab. This homework is your chance!
(Note: it may be possible to provide answers for this homework without actually completing one of the tutorials – but this is not
recommended…your chosen tutorial will be duly noted and may come back to haunt you on the Final Exam!!)
1. Visit this website: http://www.openhelix.com/sponsored.shtml (several tutorials are offered for free!)

GeneSNPs - sponsored by the National Institute of Environmental Health Sciences (NIEHS)


Genome Variation Server (GVS)
- sponsored by the National Heart, Lung, and Blood Institute (NHLBI)
& Univ of Washington
Integrated Microbial Genomes (IMG) - sponsored by the Joint Genome Institute

SeattleSNPs
- sponsored by the National Heart, Lung, and Blood Institute (NHLBI) & Univ of
Washington

UCSC Genome Browser - sponsored by the University of California Santa Cruz Bioinformatics Group

VISTA Comparative Genomics Tools
- sponsored by Lawrence Berkeley National Laboratory
2. Choose 1 of the 6 tutorials that sounds most interesting to you.
Notice that each tutorial includes links to:



An associated web-based Genomics Resource
A set lecture PPTs (provided as a PDF file)
Exercises to give you hands-on practice with the resource
3. Complete the Exercises associated with your tutorial. You should use the Questions as your guide,
either without referring to the detailed step-by-step instructions, or following them, if you prefer.
The only Answers you are required to submit are responses to the following Questions:
 Did you learn anything new from this tutorial? If so, what?
 Did you like this tutorial? Why or why not?
 Do you think the tutorial makes “sense” without the PPT lecture?
 Would you recommend this tutorial to someone else interested in this topic?
Alternate Exercise: If none of 6 tutorials listed above interest you (??!!) – please go to the following site
http://genome.jgi-psf.org/Tutorial/Tutorial.info.html#manual & annotate any gene of your choosing – you do
NOT have to register, just “pretend” you did & follow the instructions. The only Results you are required to
submit are:
1) the gene id number & FASTA sequence for your chosen gene
2) a Functional Annotation for your gene (Note: this may be produced automatically, based on
gene structure annotation, or you may need to use functional annotation tools for which links are
provided under the Functional Annotation section.)