<![CDATA[BOL: Bioinformatics Lecture Notes]]> https://bioinformaticsonline.com/pages/view/44667/bioinformatics-lecture-notes? https://bioinformaticsonline.com/pages/view/44667/bioinformatics-lecture-notes Tue, 01 Oct 2024 03:45:26 -0500 https://bioinformaticsonline.com/pages/view/44667/bioinformatics-lecture-notes <![CDATA[Bioinformatics Lecture Notes]]> Study Resources for

ECM3413 - Bioinformatics

Contents

 

General Information

Lecture Slides

Past Exam Paper

Continuous Assessments

Suggested Reading List

General Information

bullet This module runs in Semester 2. 
bullet It is taught by Dr Ed Keedwell (Module Coordinator)
bullet Module Descriptor:  ECM3413
bullet Lecture Times: Tuesday 5pm,  171| Thursday, 171
bullet Workshop Times: Wednesday 11am Blue Room (Weeks 29,33 &40)
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Assessment: 2 CAs each worth 15% | 1 Examination worth 70%

  

Lecture Slides (if you have to print slides, to save your ink choose 'print in black and white' on the print menu)

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PPT|PDF| Lecture 1 - Introduction to Bioinformatics (& Biology)
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PPT|PDF| Lecture 2 - Genome Sequences: from fragments to sequences
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PPT|PDF| Lecture 3 - Sequence Alignment 1
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PPT|PDF| Lecture 4 - Global Pairwise Sequence Alignment
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PPT|PDF| Lecture 5 - Local Pairwise Sequence Alignment (Smith-Waterman & BLAST)
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DOC| Workshop 1 - Using BLAST and other Bioinformatics Databases
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PPT|PDF| Lecture 6 - Multiple Sequence Alignment
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PPT|PDF| Lecture 7 - BLAST (in more detail) & FASTA
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PPT|PDF| Lecture 8 - Sequence Alignment Conclusion & Other Sequence Analyses
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PPT|PDF| Lecture 9 - Markov Chains and Intro to Hidden Markov Models
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PPT|PDF| Lecture 10 - Hidden Markov Models
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PPT|PDF| Lecture 11 - Classification in Bioinformatics
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DOC|Workshop 2 - Using See5
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Workshop Data - Part 1 - adult.names | adult.data | adult.test, Part 3 - wdbc.names| wdbc.data
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PPT|PDF| Lecture 12 - Gene Expression Data
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PPT|PDF| Lecture 13 - Decision Trees and Gene Expression Classification
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PPT|PDF| Lecture 14 - Other Methods for Gene Expression Classification
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PPT|PDF| Lecture 15 - Gene Regulation
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PPT|PDF| Lecture 16 - Neural Networks in Gene Expression Analysis
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PPT|PDF| Lecture 17 - Genome Analysis
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PPT|PDF| Lecture 18 - Conclusion/Revision Lecture

 

For some reason best known to itself, my PDF creator doesn't like the slide with the substitution matrix on.  Therefore this has been removed from Lectures 3 and 7 for the PDF copy only - however, more information on these matrices can be found here.

Past Exam Paper

The paper from 2007/8 can be found here.

Continuous Assessments

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PDF|  CA1 - Manual Sequence Alignment
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PDF|Promoter.names|Promoter.data|ML.names|ML.data| CA2 - Data Mining in Bioinformatics

 

Suggested Reading List

General Bioinformatics

<="top">Xiong, J., (2006) Essential Bioinformatics, Cambridge University Press

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Lesk, A.M., (2002) Introduction to Bioinformatics, Oxford University Press
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Higgs, P.G., (2005) Bioinformatics and Molecular Evolution,  Blackwell Publishing
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Machine Learning in Bioinformatics

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Baldi, P., Brunak, S., (2001) Bioinformatics: The Machine Learning Approach, MIT Press
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Keedwell, E., Narayanan, A., (2005) Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques to Bioinformatics Problems, Wiley
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