COMP 5115 Programming Tools in Bioinformatics

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Oct 1, 2013 (3 years and 8 months ago)

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COMP 5115 Programming Tools in Bioinformatics


LAB
3


Sequence Analysis
: Sequence Alignment



Determining the similarity between two sequences is a common task in computational
biology. Starting with a nucleotide sequence for a human gene, this example use
s
alignment algorithms to locate a similar gene in another organism.

Follow the following links to investiagte each part. You will be able to wtite your own
software (in m file) to do these taks. Before writing your own
code
, first investigate the
function
s, and what they do and how they do. For example, in the first part (
Finding a
Model Organism to Study
), identfy what the function
seqshoworfs

does by typing
help
seqshoworfs
on the command window. It is also helpful to look into the content of the
functions

in
seqshoworfs
.m
.



Finding a Model Organism to Study



Use

the MATLAB Help browser to search
the Web for information.



Getting Sequence Information from a Public Database



Find the nucleotide
sequence for a human ge
ne in a public database and read the sequence
information into MATLAB.



Searching a Public Database for Related Genes
`


Find the nucleotide
sequence for a mo
use gene related to a human gene, and read the sequence
information into MATLAB.



Locating Protein Coding Sequences



Convert a sequence from nucleotides to
amino acids and identify the open reading frames.



Comparing Amino Acid Sequences



Use global and local alignment functions
to compare two amino acid sequen
ces.