Homework Assignment #1

Analyze this sequence to predict genes. RepeatMasker has already been run on the sequence, and repeats have been "soft masked" (i.e., replaced by lower-case letters). Analyze the sequence with GenScan and blastn, searching both the NR and EST databases. Also, use BLAT at the UCSC Genome Browser and see what you can learn.

Write (in a plain text file) a summary of your gene predictions, no more than half a page, describing the evidence for them. Explain what you learned about which tissues express the gene (or genes). Send your report by email to Qingyu Wang (qzw102@psu.edu) by noon on Monday. I'll be available most of Friday to answer questions, at webb@bx.psu.edu, 865-4551, or in 506B Wartik Lab.

In class today, sign up to see me for 15 minutes next Monday or next Tuesday morning. We will use the 15 minutes to discuss possible class projects.

(This page is available as: http:www.bx.psu.edu/courses/bx-fall10/assign1.html)