Difference between revisions of "BIN-SEQA-Comparison"

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<div id="BIO">
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<div id="ABC">
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Sequence Analysis: Comparison
 
Sequence Analysis: Comparison
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  </div>
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Sequence analysis by comparison; deterministic pattern matching; probabilistic pattern matching; HMMS; Neural Networks)
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  {{Vspace}}
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
−
Sequence analysis by comparison; deterministic pattern matching; probabilistic pattern matching; HMMS; Neural Networks
 
 
</div>
 
</div>
  
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{{Vspace}}
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{{Smallvspace}}
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−
 
 
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__TOC__
 
−
 
 
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{{Vspace}}
 
−
 
 
−
 
 
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{{DEV}}
 
−
 
 
−
{{Vspace}}
 
  
  
 +
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
 +
<div style="font-size:118%;">
 +
<b>Abstract:</b><br />
 +
<section begin=abstract />
 +
Sequence analysis by pattern matching.
 +
<section end=abstract />
 
</div>
 
</div>
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<div id="ABC-unit-framework">
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<!-- ============================  -->
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== Abstract ==
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<hr>
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<!-- included from "../components/BIN-SEQA-Comparison.components.wtxt", section: "abstract" -->
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<table>
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...
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<tr>
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<td style="padding:10px;">
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{{Vspace}}
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<b>Objectives:</b><br />
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+
This unit will ...
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* ... introduce the concepts of deterministic and probabilistic pattern matching;
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== This unit ... ==
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* ... demonstrate some applications in the online suite of EMBOSS tools.
−
=== Prerequisites ===
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</td>
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<!-- included from "../components/BIN-SEQA-Comparison.components.wtxt", section: "prerequisites" -->
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<td style="padding:10px;">
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<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
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<b>Outcomes:</b><br />
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You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:
+
After working through this unit you ...
−
<!-- included from "FND-prerequisites.wtxt", section: "biomolecules" -->
+
* ... are familar with the ideas of deterministic and probabilistic pattern matching, and how the latter relates to machine learning.
 +
</td>
 +
</tr>
 +
</table>
 +
<!-- ============================ -->
 +
<hr>
 +
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 +
<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>
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:<br />
 
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
 
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
−
<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
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This unit builds on material covered in the following prerequisite units:<br />
−
You need to complete the following units before beginning this one:
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*[[BIN-SEQA-Concepts|BIN-SEQA-Concepts (Concepts of Sequence Analysis)]]
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*[[BIN-SEQA-Concepts]]
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<section end=prerequisites />
 +
<!-- ============================  -->
 +
</div>
  
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{{Vspace}}
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{{Smallvspace}}
  
  
−
=== Objectives ===
 
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<!-- included from "../components/BIN-SEQA-Comparison.components.wtxt", section: "objectives" -->
 
−
...
 
  
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{{Vspace}}
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{{Smallvspace}}
  
  
−
=== Outcomes ===
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__TOC__
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<!-- included from "../components/BIN-SEQA-Comparison.components.wtxt", section: "outcomes" -->
 
−
...
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
=== Deliverables ===
 
−
<!-- included from "../components/BIN-SEQA-Comparison.components.wtxt", section: "deliverables" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
−
*<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.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
−
*<b>Journal</b>: Document your progress in your [[FND-Journal|course journal]].
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
−
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|insights! page]].
 
  
 
{{Vspace}}
 
{{Vspace}}
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=== Evaluation ===
 
=== Evaluation ===
−
<!-- included from "../components/BIN-SEQA-Comparison.components.wtxt", section: "evaluation" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "eval-none" -->
 
 
<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
−
:This unit is not evaluated for course marks.
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
−
 
 
−
{{Vspace}}
 
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−
 
 
−
</div>
 
−
<div id="BIO">
 
 
== Contents ==
 
== Contents ==
−
<!-- included from "../components/BIN-SEQA-Comparison.components.wtxt", section: "contents" -->
 
 
{{Task|1=
 
{{Task|1=
 
*Read the introductory notes on {{ABC-PDF|BIN-SEQA-Comparison|"Comparison" as a paradigm for sequence analysis}}.
 
*Read the introductory notes on {{ABC-PDF|BIN-SEQA-Comparison|"Comparison" as a paradigm for sequence analysis}}.
 
}}
 
}}
 +
 +
<!-- biostrings matchPattern() and friends, countPattern() and friends, matchPWM() and friendsturn PWM into PSSM with a random model -->
  
  
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;Local composition
 
;Local composition
 
# Find <code>pepinfo</code> under the '''PROTEIN COMPOSITION''' heading.
 
# Find <code>pepinfo</code> under the '''PROTEIN COMPOSITION''' heading.
−
# Retrieve the YFO Mbp1 related sequence from your '''R''' database, e.g. with something like <br /><code>  cat(db$protein[db$protein$name == "UMAG_1122"), "sequence"]</code>
+
# Retrieve the MYSPE Mbp1 related sequence from your '''R''' database, e.g. with something like <br /><code>  cat(db$protein[db$protein$name == "UMAG_1122"), "sequence"]</code>
 
# Copy and paste the sequence into the input field.
 
# Copy and paste the sequence into the input field.
 
# Run with default parameters.
 
# Run with default parameters.
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# Do the same in a separate window for yeast Mbp1.
 
# Do the same in a separate window for yeast Mbp1.
 
# Try to compare ... <small>(kind of hard without reference, overlay and expectation, isn't it?)</small>
 
# Try to compare ... <small>(kind of hard without reference, overlay and expectation, isn't it?)</small>
−
}}
 
−
 
−
 
−
{{task|1=
 
−
;Global composition
 
−
# Find <code>pepstats</code> under the '''PROTEIN COMPOSITION''' heading.
 
−
# Paste the YFO Mbp1 sequence into the input field.
 
−
# Run with default parameters.
 
−
# Do the same in a separate window for yeast Mbp1.
 
−
# Try to compare ... are there significant and unexpected differences?
 
 
}}
 
}}
  
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;Motifs
 
;Motifs
 
# Find <code>pepcoil</code>, an algorithm to detect {{WP|coiled coil}} motifs.
 
# Find <code>pepcoil</code>, an algorithm to detect {{WP|coiled coil}} motifs.
−
# Run this with the YFO Mbp1 sequence and yeast Mbp1.
+
# Run this with the MYSPE Mbp1 sequence and yeast Mbp1.
 
# Try to compare ... do both sequences have coiled-coil motif predictions? Are they annotated in approximately comparable regions of the respective sequence?
 
# Try to compare ... do both sequences have coiled-coil motif predictions? Are they annotated in approximately comparable regions of the respective sequence?
 
}}
 
}}
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;Transmembrane sequences
 
;Transmembrane sequences
 
# Find <code>tmap</code>. Also find <code>shuffleseq</code>.
 
# Find <code>tmap</code>. Also find <code>shuffleseq</code>.
−
# Use your YFO sequence to annotate transmembrane helices for your protein and for a few shuffled sequences. The YFO is not expected to have TM helices, nor are the shuffled sequences expected to have any. If you '''do''' find some, these are most likely "''false positives''".
+
# Use your MYSPE sequence to annotate transmembrane helices for your protein and for a few shuffled sequences. The MYSPE is not expected to have TM helices, nor are the shuffled sequences expected to have any. If you '''do''' find some, these are most likely "''false positives''".
  
 
# Also compare the following positive control: Gef1 - a yeast chloride channel with 10 trans-membrane helices and outward localized N-terminus:
 
# Also compare the following positive control: Gef1 - a yeast chloride channel with 10 trans-membrane helices and outward localized N-terminus:
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# Evaluate the output: does the algorithm (wrongly) predict TM-helices in your protein? In the shuffled sequences? Does it find all ten TM-helices in Gef1?
 
# Evaluate the output: does the algorithm (wrongly) predict TM-helices in your protein? In the shuffled sequences? Does it find all ten TM-helices in Gef1?
−
}}
 
−
 
−
 
−
Try to familiarize yourself with the offerings in the EMBOSS package. I find some of the nucleic acid tools indispensable in the lab, such as restriction-site mapping tools, and I frequently use the alignment tools <code>Needle</code> and <code>Water</code>, but by and large the utility of many of the components&ndash;while fast, efficient and straightforward to use&ndash; suffers from lack of reference and comparison and from terse output. The routines show their conceptual origin in the 1970s and 1980s. We will encounter alternatives in later assignments.
 
−
 
−
{{Vspace}}
 
−
 
−
=='''R''' Sequence Analysis Tools==
 
−
 
−
It's interesting to see this collection of tools that were carefully designed some twenty years ago, as an open source replacement for a set of software tools - the GCG package - that was indispensable for molecular biology labs in the 80s and 90s, but whose cost had become prohibitive. Fundamentally this is a building block approach, and the field has turned to programming solutions instead.
 
−
 
−
As for functionality, much more sophisticated functions are available on the Web: do take a few minutes and browse the [http://bioinformatics.ca/links_directory/tag/protein-sequence-analysis curated Web services directory of bioinformatics.ca].
 
−
 
−
As for versatility, '''R''' certainly has the edge. Let's explore some of the functions available in the <code>seqinr</code> package that you already encountered in the introductory [[R tutorial]]. They are comparatively basic - but it is easy to prepare our own analysis.
 
  
−
 
−
{{Vspace}}
 
−
 
−
{{task|1 =
 
−
* Study the code in the <code>Sequence Analysis</code> section of the '''R''' script
 
 
}}
 
}}
  
  
 +
Try to familiarize yourself with the offerings in the EMBOSS package. I find some of the nucleic acid tools indispensable in the lab, such as restriction-site mapping tools (remap), and I frequently use the alignment tools <code>Needle</code> and <code>Water</code>, but by and large the utility of many of the components&ndash;while fast, efficient and straightforward to use&ndash; suffers from lack of reference and comparison and from terse output. The routines show their conceptual origin in the 1970s and 1980s.
  
−
{{Vspace}}
+
It's interesting to consider how this collection of tools that were carefully designed some thirty years ago, as an open source replacement for a set of software tools - the GCG package - that was indispensable for molecular biology labs in the 80s and 90s, but whose cost had become prohibitive - has slowly lost relevance due to a change in computational paradigms. Everything these tools do is still correct. But fundamentally this is a building block approach, and the field has turned to programming solutions instead - as exemplified in seqinr and other R packages, and the Bioconductor project.
−
 
 
−
 
 
−
== Further reading, links and resources ==
 
−
<!-- {{#pmid: 19957275}} -->
 
−
<!-- {{WWW|WWW_GMOD}} -->
 
−
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
  
 
{{Vspace}}
 
{{Vspace}}
  
−
 
−
== Notes ==
 
−
<!-- included from "../components/BIN-SEQA-Comparison.components.wtxt", section: "notes" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "notes" -->
 
−
<references />
 
  
 
{{Vspace}}
 
{{Vspace}}
  
−
 
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</div>
 
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<div id="ABC-unit-framework">
 
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== Self-evaluation ==
 
−
<!-- included from "../components/BIN-SEQA-Comparison.components.wtxt", section: "self-evaluation" -->
 
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<!--
 
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=== Question 1===
 
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Question ...
 
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<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 
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<div class="mw-collapsible-content">
 
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Answer ...
 
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<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_ask" -->
 
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----
 
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{{Vspace}}
 
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<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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----
 
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<div class="about">
 
<div class="about">
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-08-05
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:2020-09-24
 
<b>Version:</b><br />
 
<b>Version:</b><br />
−
:0.1
+
:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*1.1  Maintenance. Removed obsolete bioinformatics.ca link.
 +
*1.0  First live version
 
*0.1 First stub
 
*0.1 First stub
 
</div>
 
</div>
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[[Category:ABC-units]]
 
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<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_footer" -->
 
  
 
{{CC-BY}}
 
{{CC-BY}}
  
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[[Category:ABC-units]]
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{{UNIT}}
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{{LIVE}}
 
</div>
 
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<!-- [END] -->
 
<!-- [END] -->

Latest revision as of 15:54, 24 September 2020

Sequence Analysis: Comparison

(Sequence analysis by comparison; deterministic pattern matching; probabilistic pattern matching; HMMS; Neural Networks)


 


Abstract:

Sequence analysis by pattern matching.

Objectives:
This unit will ...

  • ... introduce the concepts of deterministic and probabilistic pattern matching;
  • ... demonstrate some applications in the online suite of EMBOSS tools.

Outcomes:
After working through this unit you ...

  • ... are familar with the ideas of deterministic and probabilistic pattern matching, and how the latter relates to machine learning.

Deliverables:

  • Time management: 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.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

    • Prerequisites:
    You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:

    • Biomolecules: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.

    This unit builds on material covered in the following prerequisite units:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Task:



     


    Analyze

    Let us perform a few simple sequence analyses using the online EMBOSS tools. EMBOSS (the European Molecular Biology laboratory Open Software Suite) combines a large number of simple but fundamental sequence analysis tools. The tools can be installed locally on your own machine, or run via a public Web interface. Google for EMBOSS explorer, public access points include http://emboss.bioinformatics.nl/ .

    Access an EMBOSS Explorer service and explore some of the tools:


    Task:

    Local composition
    1. Find pepinfo under the PROTEIN COMPOSITION heading.
    2. Retrieve the MYSPE Mbp1 related sequence from your R database, e.g. with something like
      cat(db$protein[db$protein$name == "UMAG_1122"), "sequence"]
    3. Copy and paste the sequence into the input field.
    4. Run with default parameters.
    5. Scroll to the figures all the way at the bottom.
    6. Do the same in a separate window for yeast Mbp1.
    7. Try to compare ... (kind of hard without reference, overlay and expectation, isn't it?)


    Task:

    Motifs
    1. Find pepcoil, an algorithm to detect coiled coil motifs.
    2. Run this with the MYSPE Mbp1 sequence and yeast Mbp1.
    3. Try to compare ... do both sequences have coiled-coil motif predictions? Are they annotated in approximately comparable regions of the respective sequence?


    Task:

    Transmembrane sequences
    1. Find tmap. Also find shuffleseq.
    2. Use your MYSPE sequence to annotate transmembrane helices for your protein and for a few shuffled sequences. The MYSPE is not expected to have TM helices, nor are the shuffled sequences expected to have any. If you do find some, these are most likely "false positives".
    1. Also compare the following positive control: Gef1 - a yeast chloride channel with 10 trans-membrane helices and outward localized N-terminus:
    >gi|6322500|ref|NP_012574.1| Gef1p [Saccharomyces cerevisiae S288c]
MPTTYVPINQPIGDGEDVIDTNRFTNIPETQNFDQFVTIDKIAEENRPLSVDSDREFLNSKYRHYREVIW
DRAKTFITLSSTAIVIGCIAGFLQVFTETLVNWKTGHCQRNWLLNKSFCCNGVVNEVTSTSNLLLKRQEF
ECEAQGLWIAWKGHVSPFIIFMLLSVLFALISTLLVKYVAPMATGSGISEIKVWVSGFEYNKEFLGFLTL
VIKSVALPLAISSGLSVGKEGPSVHYATCCGYLLTKWLLRDTLTYSSQYEYITAASGAGVAVAFGAPIGG
VLFGLEEIASANRFNSSTLWKSYYVALVAITTLKYIDPFRNGRVILFNVTYDRDWKVQEIPIFIALGIFG
GLYGKYISKWNINFIHFRKMYLSSWPVQEVLFLATLTALISYFNEFLKLDMTESMGILFHECVKNDNTST
FSHRLCQLDENTHAFEFLKIFTSLCFATVIRALLVVVSYGARVPAGIFVPSMAVGATFGRAVSLLVERFI
SGPSVITPGAYAFLGAAATLSGITNLTLTVVVIMFELTGAFMYIIPLMIVVAITRIILSTSGISGGIADQ
MIMVNGFPYLEDEQDEEEEETLEKYTAEQLMSSKLITINETIYLSELESLLYDSASEYSVHGFPITKDED
KFEKEKRCIGYVLKRHLASKIMMQSVNSTKAQTTLVYFNKSNEELGHRENCIGFKDIMNESPISVKKAVP
VTLLFRMFKELGCKTIIVEESGILKGLVTAKDILRFKRIKYREVHGAKFTYNEALDRRCWSVIHFIIKRF
TTNRNGNVI
    1. Evaluate the output: does the algorithm (wrongly) predict TM-helices in your protein? In the shuffled sequences? Does it find all ten TM-helices in Gef1?


    Try to familiarize yourself with the offerings in the EMBOSS package. I find some of the nucleic acid tools indispensable in the lab, such as restriction-site mapping tools (remap), and I frequently use the alignment tools Needle and Water, but by and large the utility of many of the components–while fast, efficient and straightforward to use– suffers from lack of reference and comparison and from terse output. The routines show their conceptual origin in the 1970s and 1980s.

    It's interesting to consider how this collection of tools that were carefully designed some thirty years ago, as an open source replacement for a set of software tools - the GCG package - that was indispensable for molecular biology labs in the 80s and 90s, but whose cost had become prohibitive - has slowly lost relevance due to a change in computational paradigms. Everything these tools do is still correct. But fundamentally this is a building block approach, and the field has turned to programming solutions instead - as exemplified in seqinr and other R packages, and the Bioconductor project.


     


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-24

    Version:

    1.1

    Version history:

    • 1.1 Maintenance. Removed obsolete bioinformatics.ca link.
    • 1.0 First live version
    • 0.1 First stub

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-SEQA-Comparison&oldid=11641"