Introduction to Bioinformatics

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Oct 1, 2013 (4 years and 13 days ago)

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Introduction to Bioinformatics

Homework 2


Part
I
:

1.

Download two hemoglobin sequences (accession# AY885671, AY885672) from
Genbank.

http://www.ncbi.nlm.nih.gov/entrez
/viewer.fcgi?db=nucleotide&val=58429967

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=58429966


2.

Save the FASTA format of the sequences to a file.

Name the file hemoglobin.fasta.

(choose FASTA in the
Display

field and click
Send

button to save the sequence to a
file.)

3.

Write a Perl program called Perl2a.pl which (1) reads the two sequences from the file,
(2) calculates the frequency of nucleotides fo
r each sequence and (3) prints out the
results to STDOUT.


The output should look like:

>gi|58429967…


#definition line

Count of A = 23;



>gi|…

Count of A = 34;




Part
I
I:

1.

Download from the Genbank the sequence for Homo sapiens dopamine transporter
(S
LC6A3) (accession #M95167) and save the FASTA format of the sequence to a file
named dopamine_transporter.fasta.

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucl
eotide&val=703094


2.

Write a Perl program called perl2b.pl which (1) constructs an associate array for the
standard genetic code

(
you may find a table for the code here
:
http://www.cs.uakron.edu/~zduan/class/bioinformatics/Homework/Codon.dat
)
; (2)
translates the coding part of the sequence to obtain the protein sequence; The coding
sequence starts at the 129th base and ends at 1991; (3) outputs the FASTA format of
the re
sulting sequence to STDOUT.

3.

Compare your results with the sequence at Genbank.


Submission
: When you are ready to submit, obtain a printed copy of the required
materials. Turned in the hard copy to the instructor by the start of class on the date the
homew
ork is due. You must also email the program(s) to your instructor. Identify the
email with the subj
ect: Bioinformatics Assignment 2

(Your name) and
be sure that your
name appears on the subject line
. Be sure to email your
working

solution before the due
da
te! Do not submit non
-
working programs.