Homework
HW1. Download and install
Perl (for windows http://www.activestate.com/)
Write a Perl program that reads a number k from keyboard and prints “Hello,
World!” k times in the following
format:
…
For Perl tutorials see http://www.sthomas.net/roberts-perl-tutorial.htm
Due:
9/25 at 8am via email (Xijin.Ge@sdstate.edu)
HW2. Page 118, Part II &
Page 119 Part IV of textbook
Also write a short paragraph to
describe what you get.
Due:
10/2 at 8am via email as a MS Word or PDF file.
HW3. Problems #1 & #2,
Page 222.
Due: 8am on Oct. 9 via email as a MS
Word or PDF file.
HW4. All
problems in Chapter 2.
Due:
9pm Oct. 15 via email. Please name your file “HW4_xxxx.doc” or
“HW4_xxxx.pdf” where
xxxx is your first name.
HW5. Write a
program that reads two sequence files (in FASTA format) and perform the dot matrix
alignment. Your output file should contain the coordinates of the matched base
pairs. Send me the properly commented
program only. I will test your program with my own sequence files.
Due: 9pm Oct. 22 via email. Please name
your file “HW5_XXX.pl”.
HW6. Problem #5 in page 223.
Due: 9pm Nov 13 via email.
HW7. This file contains a list
of 322 unknown sequences. All of them are from one particular species.
(a) Determine which
species these sequences come from.
(b) Based on the
species information, BLAST these 322 sequences against UniGene database to
annotate these sequences, i.e., find out the genes that these sequences could
be aligned to.
Your final results should be presented as
an Excel table with three columns: the ID of the 322 sequences, the gene
symbol, and gene title. Also provide about one page of documentation on how you
obtained these results, with details as to what options/parameters were used
for BLAST and why you made that choice. If you created any scripts or programs
to process the data, also send in the program.
Due: 11pm Nov 23 via email. For this
group mini-project, only one submission is required.