View source for BIN-ALI-Similarity

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Measuring Sequence Similarity
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(sequence similarity: measurement via MDM; BLOSUM 62 matrix, affine gap penalties)
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<b>Abstract:</b><br />
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In order to compare protein sequences quantitatively, we must define how to measure the similarity of two amino acids. This can be done according to biophysical considerations, or empirically, based on the propensity of amino acids to substitute for each other in homologous sequences. "Mutation Data Matrices" make this information conveniently available.
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<b>Objectives:</b><br />
This unit will ...
* ... introduce issues of defining amino acid similarity;
* ... teach how to use the amino acid property tables included in the <tt>seqinr::</tt> package;
* ... teach the use of mutation data matrices from the Biostrings package.
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<b>Outcomes:</b><br />
After working through this unit you ...
* ... can access and work with amino acid property tables from the <tt>seqinr::</tt> package;
* ... can access and work with mutation data matrices from the <tt>Biostrings::</tt> package, in particular <tt>BLOSUM62</tt>.
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<b>Deliverables:</b><br />
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<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
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<b>Prerequisites:</b><br />
This unit builds on material covered in the following prerequisite units:<br />
*[[RPR-Biostrings|RPR-Biostrings (The biostrings R Package)]]
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__TOC__

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=== Evaluation ===
<b>Evaluation: NA</b><br />
<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
== Contents ==

{{Task|1=
*Read the introductory notes on {{ABC-PDF|BIN-ALI-Similarity|the concepts behind quantifying amino acid sequence similarity}}.
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The NCBI makes its alignment matrices available by ftp. They are located at  ftp://ftp.ncbi.nih.gov/blast/matrices - for example here is a link to the [ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62 '''BLOSUM62 matrix''']<ref>That directory also contains sourcecode to generate the PAM matrices. This may be of interest if you ever want to produce scoring matrices from your own datasets.</ref>.

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BLOSUM62

   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  J  Z  X  *
A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1 -1 -1 -4
R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1 -2  0 -1 -4
N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  4 -3  0 -1 -4
D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4 -3  1 -1 -4
C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -1 -3 -1 -4
Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0 -2  4 -1 -4
E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1 -3  4 -1 -4
G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -4 -2 -1 -4
H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0 -3  0 -1 -4
I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3  3 -3 -1 -4
L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4  3 -3 -1 -4
K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0 -3  1 -1 -4
M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3  2 -1 -1 -4
F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3  0 -3 -1 -4
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -3 -1 -1 -4
S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0 -2  0 -1 -4
T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1 -1 -1 -4
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -2 -2 -1 -4
Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -1 -2 -1 -4
V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3  2 -2 -1 -4
B -2 -1  4  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4 -3  0 -1 -4
J -1 -2 -3 -3 -1 -2 -3 -4 -3  3  3 -3  2  0 -3 -2 -1 -2 -1  2 -3  3 -3 -1 -4
Z -1  0  0  1 -3  4  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -2 -2 -2  0 -3  4 -1 -4
X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -4
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1

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{{task|
* Study this and make sure you understand what this table is, how it can be used, and what a reasonable range of values for identities and pairscores for non-identical, similar and dissimilar residues is. Ask on the mailing list in case you have questions. '''This piece of data is the foundation of any sequence alignment. without it, no sensible alignment could be produced!'''
* Figure out the following values:
** Compare an identical match of histidine with an identical match of serine. What does this mean?
** How similar are lysine and leucine, as compared to leucine and isoleucine? Is this what you expect?
** PAM matrices are sensitive to an interesting artefact. Since W and R can be interchanged with a single point mutation, the probability of observing W&rarr;R and R&rarr;W exchanges in '''closely related sequences''' is much higher than one would expect from the two amino acid's biophysical properties. (Why?) PAM matrices were compiled from hypothetical point exchanges and then extrapolated. Therefore these matrices assign a relatively high degree of similarity to (W, R), that is not warranted considering what actually happens in nature. Do you see this problem in the BLOSUM matrix? If BLOSUM does not have this issue, why not?
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{{ABC-unit|BIN-ALI-Similarity.R}}

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== Further reading, links and resources ==

*{{#pmid: 15286655}}
*{{WP|BLOSUM|'''BLOSUM''' article at Wikipedia}} (Good article.)

== Notes ==
<references />

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<div class="about">
<b>About ... </b><br />
&nbsp;<br />
<b>Author:</b><br />
:Boris Steipe <boris.steipe@utoronto.ca>
<b>Created:</b><br />
:2017-08-05
<b>Modified:</b><br />
:2020-09-24
<b>Version:</b><br />
:1.1
<b>Version history:</b><br />
*1.1 2020 Updates
*1.0 First live version
*0.1 First stub
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